My lab would love to use your program instead of FreeSurfer to speed up our pre-proces

<a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="/us

We use the files listed in <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAll

Hi <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="

Thanks <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-u

Integrate with fmriprep,about deep-mi/fastsurfer

Comments (23)

m-reuter commented on July 29, 2024 2

we are generating the T1.mgz since a while anyway. Also we create now a few symlinks at the end e.g. to point to wmparc and aparc+aseg (although we use the DKT altlas definition which merge a few lables).
Does anyone know if fmriprep is working with FastSurfer currently or are there other files that are needed?

from fastsurfer.

pcamach2 commented on July 29, 2024 1

@m-reuter, I ran some tests in February using the stable version of FastSurfer available at the time (nipreps/smriprep#278), which failed to complete sMRIPrep when treating those FastSurfer outputs as an existing FreeSurfer directory. I am running some tests now using the current dev branch of FastSurfer, which I will update in this thread!

from fastsurfer.

effigies commented on July 29, 2024 1

Sounds great. Sorry, I completely forgot that you'd started work on this. Please feel free to bug me repeatedly as my notifications get quickly buried. I'll try to make a point of monitoring sMRIPrep more closely.

from fastsurfer.

m-reuter commented on July 29, 2024

Is there a list of what files need to be there ?

from fastsurfer.

effigies commented on July 29, 2024

We use the files listed in https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 to determine if a step has been completed.

The table is constructed here: https://github.com/nipy/nipype/blob/5116ee208205c8050f87fc2a45bb0f35e3dd1c0a/nipype/interfaces/freesurfer/preprocess.py#L1069-L1321

If there are different build targets between the two pipelines, then this approach is not going to work. What might be useful is a way to detect whether a subject was processed to completion with FastSurfer.

from fastsurfer.

m-reuter commented on July 29, 2024

Hi @effigies

we write a file recon-surf.done when the pipeline completes. Depending on the flags that the user users during processing, there will be different files available at finish.

What would be helpful is a list of the files that are actually needed by fmriprep as it surely does not need all freesurfer outputs. We can then let you know which files are equivalent or can provide scripts that generate the missing files.

from fastsurfer.

m-reuter commented on July 29, 2024

Will close this due to inactivity. Can reopen if a list with filenames is provided.

from fastsurfer.

effigies commented on July 29, 2024

fMRIPrep only really uses the ?h.{pial,smoothwm,inflated} and mri_vol2surf and mri_surf2surf need to be able to target fsaverage*, so I think ?h.sphere.reg or similar.

from fastsurfer.

m-reuter commented on July 29, 2024

Thanks @effigies , all these should be available if you run FastSurfer with the --surfreg flag to construct the spherical atlas registrations also (which would be needed also for group analysis on the cortex).

from fastsurfer.

effigies commented on July 29, 2024

Oh, we do also need T1.mgz, to account for any rigid differences between the input T1w files and what FreeSurfer has. (Usually only happens with multiple T1w files.) I assume that's still there?

from fastsurfer.

m-reuter commented on July 29, 2024

We don't need the T1 and therefore don't create it. In FreeSurfer it is used for the watershed (skull stripping) and we already get a full segmentation on the full-head images and create brainmask from the segmentation. Just use the nu.mgz instead which we create.
Also note that FreeSurfer only reslices the input T1w to be conform but keeps coordinates the same, meaning you can get back to the original T1w anytime from any image, because the information is in the headers (e.g. with mri_convert -rl rawT1w.nii.gz -rt linear,cubic,nearest input output ).

from fastsurfer.

m-reuter commented on July 29, 2024

@effigies just to ping this topic again. You should not need the T1.mgz. It is an intermediate file in the FS pipeline and should not be looked at for anything. Probably someone thought it is important because of its name.
If it (or rather the image header) is only needed to map FS results back to original input space (your description sounded like that is the case?) then you can take any other image in the FreeSurfer stream for that. I would recommend the orig.mgz as it is the first image in FreeSurfer space without any other processing.

from fastsurfer.

effigies commented on July 29, 2024

We actually run mri_robust_register against the T1.mgz not merely check the header, as we ran across situations where people were using precomputed derivatives that were, for some reason, out of register with the inputs.

We run this after N4 correction, so T1.mgz does seem more comparable than orig.mgz, but except in really severe cases, that's probably fine.

from fastsurfer.

m-reuter commented on July 29, 2024

OK, what exactly do you register with the T1.mgz? If it is the original scan, the reslicing matrix between that image and the FreeSurfer conform space is in the image headers, so no registration would be necessary (and could lead to misalignment). FreeSurfer does not change world coordinates, only reslices to conform 1mm isotropic voxels.

For example, to map a segmentation back to the original input image:
mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg_in_input_space.mgz

This maps aseg.mgz into the original input space (rawavg.mgz is in the original input space). -rl is "reslice like" and -rt "resample type", here nearest neighbour interpolation for segmentation. Note, that usually it is a bad idea to map a segmentation due to the interpolation artefacts and should be avoided. If it is needed for ROI analysis, you could also map the other image into freesurfer conform space:
mri_convert -rl orig.mgz -rt cubic <whatever in original input space> <new name in FS conform space>.
A registration is only necessary if you have a 3rd space (e.g. an fMRI image or something else). Depending on what it is, you could use various registration approaches (e.g. bbregister for fMRI).

Happy to setup a quick meeting to chat about this, if you like.

from fastsurfer.

effigies commented on July 29, 2024

What we do is:

INU correct all incoming T1w images
mri_robust_template the corrected images to create our "subject template"
Pass the subject template to FreeSurfer, use recon-all -autorecon1 -noskullstrip
Register our subject template to T1.mgz

If fMRIPrep runs FreeSurfer (the user doesn't provide pre-computed FreeSurfer derivatives), then the two images are obviously in register. If there is only one T1w input or both FreeSurfer and fMRIPrep chose the same image as the first time-point, then the two images are in register. If there are multiple and the order differed, or in any other way the two images are not in alignment, then simply reslicing isn't going to do the trick.

from fastsurfer.

m-reuter commented on July 29, 2024

I see. I would recommend to use nu.mgz as the registration target in that case (as it is also NU corrected but not further processed like the T1.mgz). Should be more similar to your template image. Probably orig.mgz would also work, but it is not NU corrected if the user provided it.

from fastsurfer.

pcamach2 commented on July 29, 2024

As an update, using the FastSurfer outputs as an existing FreeSurfer directory in sMRIPrep fails (for all datasets I have tested) due to a missing file mri/aseg.auto_noCCseg.label_intensities.txt during the autorecon3 step as follows:

 resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220419-11:59:59,921 nipype.workflow WARNING:
	 Storing result file without outputs
220419-11:59:59,928 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" (/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3)
220419-12:00:00,612 nipype.workflow ERROR:
	 Node autorecon3 failed to run on host host-machine.
220419-12:00:00,618 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB577/log/20220419-093910_411669c1-a518-439f-b581-40175e148f47/crash-20220419-120000-pcamach2-autorecon3-ef2cb235-7a77-4bba-aceb-70df30898c91.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
    raise RuntimeError(
RuntimeError: Command:
recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /opt/scratch/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 pcamach2 redacted_redacted_access 422749 Apr 19 11:50 /opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.log
Linux redacted-redacted-14 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.local-copy'
#-----------------------------------------
#@# AParc-to-ASeg aparc Tue Apr 19 11:59:21 CDT 2022
/opt/scratch/freesurfer/sub-SUB577

 mri_aparc2aseg --s sub-SUB577 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /opt/scratch/freesurfer
subject sub-SUB577
outvol /opt/scratch/freesurfer/sub-SUB577/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/lh.white

Reading lh pial surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/lh.pial

Loading lh annotations from /opt/scratch/freesurfer/sub-SUB577/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/rh.white

Reading rh pial surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/rh.pial

Loading rh annotations from /opt/scratch/freesurfer/sub-SUB577/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /opt/scratch/freesurfer/sub-SUB577/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /opt/scratch/freesurfer/sub-SUB577/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mri_aparc2aseg: could not read mri/aseg.auto_noCCseg.label_intensities.txt
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.56
No such file or directory
Linux redacted-redacted-14 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-SUB577 exited with ERRORS at Tue Apr 19 11:59:59 CDT 2022

For more details, see the log file /opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

220419-12:00:02,607 nipype.workflow ERROR:
	 could not run node: smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3
Preprocessing did not finish successfully. Errors occurred while processing data from participants: SUB577 (1). Check the HTML reports for details.

Run command:

singularity run --nv -B ./bids:/data,./bids/derivatives:/out,/path/redacted/singularity_images/fslicense/license.txt:/opt/freesurfer/license.txt,./bids/derivatives/fastsurfer:/opt/scratch/freesurfer /path/redacted/singularity_images/smriprep/smriprep.sif /data/ /out/ --fs-subjects-dir /opt/scratch/freesurfer --fs-license-file /opt/freesurfer/license.txt participant --participant-label sub-SUB577

Terminal output:

/opt/conda/lib/python3.8/site-packages/bids/layout/models.py:148: FutureWarning: The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
  warnings.warn("The 'extension' entity currently excludes the leading dot ('.'). "
220419-09:39:13,225 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.8.3:
      * BIDS dataset path: /data.
      * Participant list: ['SUB577'].
      * Run identifier: 20220419-093910_411669c1-a518-439f-b581-40175e148f47.

    Spatial References: <none>.
    
220419-09:39:13,723 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220419-09:39:22,93 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.8.3
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.6.1
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 6.0.5.1:57b01774, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


220419-09:39:28,551 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.full_wm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/full_wm".
220419-09:39:28,557 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_norm_wf/outputnode".
220419-09:39:28,572 nipype.workflow INFO:
	 [Node] Running "full_wm" ("nipype.interfaces.utility.wrappers.Function")
220419-09:39:28,635 nipype.workflow INFO:
	 [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
220419-09:39:28,699 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_norm_wf.outputnode".
220419-09:39:28,877 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
220419-09:39:28,906 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
220419-09:39:28,912 nipype.workflow INFO:
	 [Node] Running "lap_tmpl" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1
220419-09:39:28,996 nipype.workflow INFO:
	 [Node] Running "res_tmpl" ("niworkflows.interfaces.nibabel.RegridToZooms")
220419-09:39:29,796 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.full_wm".
220419-09:39:31,168 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl".
220419-09:39:31,658 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.bidssrc" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/bidssrc".
220419-09:39:31,679 nipype.workflow INFO:
	 [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
220419-09:39:31,725 nipype.interface INFO:
	 No "roi" images found for sub-<undefined>
220419-09:39:31,747 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.bidssrc".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220419-09:39:34,349 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
220419-09:39:35,997 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220419-09:39:36,137 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.fs_isrunning" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/fs_isrunning".
220419-09:39:37,548 nipype.workflow INFO:
	 [Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
220419-09:39:37,649 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions".
220419-09:39:39,279 nipype.workflow INFO:
	 [Node] Running "fs_isrunning" ("nipype.interfaces.utility.wrappers.Function")
220419-09:39:39,395 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.fs_isrunning".
220419-09:39:39,900 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
220419-09:39:40,122 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.t1w_conform" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_template_wf/t1w_conform".
220419-09:39:40,200 nipype.workflow INFO:
	 [Node] Setting-up "_t1w_conform0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0".
220419-09:39:40,227 nipype.workflow INFO:
	 [Node] Running "_t1w_conform0" ("niworkflows.interfaces.images.Conform")
220419-09:39:40,304 nipype.workflow INFO:
	 [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function")
220419-09:39:40,330 nipype.workflow INFO:
	 [Node] Finished "_t1w_conform0".
220419-09:39:40,343 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.t1w_conform".
220419-09:39:40,374 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources".
220419-09:39:41,769 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.get1st" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/anat_template_wf/get1st".
220419-09:39:42,213 nipype.workflow INFO:
	 [Node] Running "get1st" ("nipype.interfaces.utility.base.Select")
220419-09:39:42,289 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.anat_template_wf.get1st".
220419-09:39:44,712 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl".
220419-09:39:45,735 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl".
220419-09:39:45,746 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/fov_check".
220419-09:39:46,72 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/truncate_images".
220419-09:39:46,117 nipype.workflow INFO:
	 [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge")
220419-09:39:46,126 nipype.workflow INFO:
	 [Node] Setting-up "_truncate_images0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
220419-09:39:46,147 nipype.workflow INFO:
	 [Node] Running "_truncate_images0" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_maths.nii.gz TruncateImageIntensity /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz 0.01 0.999 256
220419-09:39:46,161 nipype.workflow INFO:
	 [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
220419-09:39:46,187 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl".
220419-09:39:46,804 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.fov_check".
220419-09:39:50,535 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/recon_config".
220419-09:39:51,215 nipype.workflow INFO:
	 [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
220419-09:39:51,451 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.recon_config".
220419-09:39:55,242 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
220419-09:39:56,613 nipype.interface INFO:
	 recon-all complete : Not running
220419-09:39:56,616 nipype.workflow INFO:
	 [Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-09:39:56,664 nipype.interface INFO:
	 recon-all complete : Not running
220419-09:39:56,889 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
220419-09:40:02,583 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm".
220419-09:40:03,486 nipype.workflow INFO:
	 [Node] Running "fsnative2t1w_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /opt/scratch/freesurfer/sub-SUB577/mri/T1.mgz --dst /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz
220419-09:40:10,364 nipype.workflow INFO:
	 [Node] Finished "_truncate_images0".
220419-09:40:10,378 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.truncate_images".
220419-09:40:12,68 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4".
220419-09:40:12,96 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n40" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
220419-09:40:12,144 nipype.workflow INFO:
	 [Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-SUB577_ses-A_T1w_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-SUB577_ses-A_T1w_maths_corrected.nii.gz --shrink-factor 4
220419-09:41:15,316 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm".
Captured warning (<class 'UserWarning'>): Reference space not set
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220419-09:41:20,699 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm".
220419-09:41:20,753 nipype.workflow INFO:
	 [Node] Running "t1w2fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --invert --outlta /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta
220419-09:41:21,130 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm".
220419-09:41:26,429 nipype.workflow INFO:
	 [Node] Finished "_inu_n40".
220419-09:41:26,457 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.inu_n4".
220419-09:41:28,168 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/lap_target".
220419-09:41:28,193 nipype.workflow INFO:
	 [Node] Running "lap_target" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_maths_corrected_maths.nii.gz Laplacian /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB577_ses-A_T1w_maths_corrected.nii.gz 1.5 1
220419-09:41:28,221 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/res_target".
220419-09:41:28,298 nipype.workflow INFO:
	 [Node] Running "res_target" ("niworkflows.interfaces.nibabel.RegridToZooms")
220419-09:41:31,961 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.res_target".
220419-09:41:34,155 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/init_aff".
220419-09:41:34,346 nipype.workflow INFO:
	 [Node] Running "init_aff" ("nipype.interfaces.ants.utils.AI"), a CommandLine Interface with command:
antsAI -c [10,1e-06,10] -d 3 -x /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_regrid.nii.gz,/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-SUB577_ses-A_T1w_maths_corrected_regrid.nii.gz,32,Regular,0.25] -o initialization.mat -p 0 -s [15,0.1] -g [40.0,0x40x40] -t Affine[0.1] -v 1
220419-09:41:53,146 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.lap_target".
220419-09:41:53,846 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/mrg_target".
220419-09:41:54,176 nipype.workflow INFO:
	 [Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge")
220419-09:41:54,244 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.mrg_target".
220419-09:42:03,398 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.init_aff".
220419-09:42:04,204 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/norm".
220419-09:42:04,265 nipype.workflow INFO:
	 [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB577_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB577_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB577_ses-A_T1w_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-SUB577_ses-A_T1w_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ]  --write-composite-transform 0
220419-09:54:13,90 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.norm".
220419-09:54:14,998 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask".
220419-09:54:15,37 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask".
220419-09:54:15,47 nipype.workflow INFO:
	 [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz --transform [ /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220419-09:54:15,101 nipype.workflow INFO:
	 [Node] Running "map_wmmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/full_wm/summap.nii.gz --interpolation Gaussian --output summap_trans.nii.gz --reference-image /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz --transform [ /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220419-09:55:07,879 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask".
220419-09:55:08,697 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask".
220419-09:55:08,828 nipype.workflow INFO:
	 [Node] Running "thr_brainmask" ("nipype.interfaces.ants.utils.ThresholdImage"), a CommandLine Interface with command:
ThresholdImage 3 /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000
220419-09:55:10,158 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask".
220419-09:55:10,722 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final".
220419-09:55:10,767 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
220419-09:55:10,809 nipype.workflow INFO:
	 [Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-SUB577_ses-A_T1w_corrected.nii.gz, sub-SUB577_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask/summap_trans.nii.gz
220419-09:55:12,435 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask".
220419-09:55:12,729 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
220419-09:55:12,760 nipype.workflow INFO:
	 [Node] Running "03_pad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10
220419-09:55:12,914 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
220419-09:55:13,56 nipype.workflow INFO:
	 [Node] Running "dil_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2
220419-09:55:14,919 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask".
220419-09:55:16,960 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask".
220419-09:55:18,800 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask".
220419-09:55:18,825 nipype.workflow INFO:
	 [Node] Running "get_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220419-09:55:22,825 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask".
220419-09:55:59,200 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0".
220419-09:55:59,243 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final".
220419-09:56:00,727 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/apply_mask".
220419-09:56:00,770 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos".
220419-09:56:00,782 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
220419-09:56:00,808 nipype.workflow INFO:
	 [Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command:
Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-SUB577_ses-A_T1w_corrected.nii.gz --likelihood-model Gaussian --mask-image /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-SUB577_ses-A_T1w_corrected_labeled.nii.gz,POSTERIOR_%02d.nii.gz] --use-random-seed 1
220419-09:56:00,810 nipype.workflow INFO:
	 [Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220419-09:56:03,174 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0".
220419-09:56:03,185 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.apply_mask".
220419-09:57:57,313 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos".
220419-09:57:58,887 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
220419-09:57:58,914 nipype.workflow INFO:
	 [Node] Running "02_pad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-SUB577_ses-A_T1w_corrected_labeled.nii.gz 10
220419-09:58:01,342 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm".
220419-09:58:08,796 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
220419-09:58:08,843 nipype.workflow INFO:
	 [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function")
220419-09:58:09,968 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels".
220419-09:58:10,813 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm".
220419-09:58:10,816 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf".
220419-09:58:10,818 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
220419-09:58:10,838 nipype.workflow INFO:
	 [Node] Running "10_me_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz ME /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz 10
220419-09:58:10,838 nipype.workflow INFO:
	 [Node] Running "05_get_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-03.nii.gz
220419-09:58:10,840 nipype.workflow INFO:
	 [Node] Running "27_depad_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz -10
220419-09:58:10,878 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm".
220419-09:58:10,990 nipype.workflow INFO:
	 [Node] Running "06_get_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02.nii.gz
220419-09:58:12,693 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf".
220419-09:58:12,858 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
220419-09:58:12,978 nipype.workflow INFO:
	 [Node] Running "apply_wm_prior" ("nipype.interfaces.utility.wrappers.Function")
220419-09:58:14,876 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm".
220419-09:58:15,424 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior".
220419-09:58:16,872 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
220419-09:58:16,878 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final".
220419-09:58:16,918 nipype.workflow INFO:
	 [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz
220419-09:58:16,923 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
220419-09:58:16,943 nipype.workflow INFO:
	 [Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-SUB577/ses-A/anat/sub-SUB577_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-SUB577_ses-A_T1w_corrected.nii.gz, sub-SUB577_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior/prodmap.nii.gz
220419-09:58:17,511 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm".
220419-09:58:18,860 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
220419-09:58:18,897 nipype.workflow INFO:
	 [Node] Running "07_fill_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz 2
220419-09:58:19,124 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm".
220419-09:58:20,856 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
220419-09:58:20,981 nipype.workflow INFO:
	 [Node] Running "26_depad_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10
220419-09:58:21,355 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf".
220419-09:58:23,13 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm".
220419-09:58:47,824 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm".
220419-09:58:48,892 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
220419-09:58:49,43 nipype.workflow INFO:
	 [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz
220419-09:58:51,625 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm".
220419-09:58:52,896 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm".
220419-09:58:52,935 nipype.workflow INFO:
	 [Node] Running "11_add_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 08_mult_gm_maths.nii.gz addtozero /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-SUB577_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz
220419-09:59:02,5 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm".
220419-09:59:02,952 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
220419-09:59:03,67 nipype.workflow INFO:
	 [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz
220419-09:59:05,42 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm".
220419-09:59:06,666 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0".
220419-09:59:06,722 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final".
220419-09:59:06,917 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
220419-09:59:06,918 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
220419-09:59:06,960 nipype.workflow INFO:
	 [Node] Running "25_depad_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10
220419-09:59:06,984 nipype.workflow INFO:
	 [Node] Running "13_add_gm_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz
220419-09:59:09,378 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm".
220419-09:59:10,913 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms".
220419-09:59:10,952 nipype.workflow INFO:
	 [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge")
220419-09:59:10,990 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms".
220419-09:59:21,653 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm".
220419-09:59:22,934 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
220419-09:59:22,934 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
220419-09:59:22,959 nipype.workflow INFO:
	 [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function")
220419-09:59:22,989 nipype.workflow INFO:
	 [Node] Running "24_depad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10
220419-09:59:23,712 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2".
220419-09:59:24,928 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7".
220419-09:59:24,959 nipype.workflow INFO:
	 [Node] Running "15_add_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz
220419-09:59:25,886 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm".
220419-09:59:33,184 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7".
220419-09:59:34,945 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7".
220419-09:59:35,21 nipype.workflow INFO:
	 [Node] Running "16_me_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2
220419-09:59:43,447 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7".
220419-09:59:45,10 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7".
220419-09:59:45,63 nipype.workflow INFO:
	 [Node] Running "17_comp_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz
220419-09:59:49,772 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7".
220419-09:59:51,15 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7".
220419-09:59:51,46 nipype.workflow INFO:
	 [Node] Running "18_md_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4
220419-09:59:55,444 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7".
220419-09:59:56,962 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7".
220419-09:59:56,991 nipype.workflow INFO:
	 [Node] Running "19_fill_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2
220419-10:00:20,836 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7".
220419-10:00:20,978 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
220419-10:00:21,28 nipype.workflow INFO:
	 [Node] Running "20_add_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220419-10:00:29,724 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2".
220419-10:00:30,998 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
220419-10:00:31,33 nipype.workflow INFO:
	 [Node] Running "21_md_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5
220419-10:00:35,274 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2".
220419-10:00:37,2 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
220419-10:00:37,52 nipype.workflow INFO:
	 [Node] Running "22_me_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5
220419-10:00:45,128 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2".
220419-10:00:47,49 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
220419-10:00:47,99 nipype.workflow INFO:
	 [Node] Running "23_depad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10
220419-10:00:49,27 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask".
220419-10:00:51,15 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform".
220419-10:00:51,52 nipype.workflow INFO:
	 [Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function")
220419-10:00:51,752 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform".
220419-10:01:08,714 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220419-10:01:08,740 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
220419-10:01:08,783 nipype.workflow INFO:
	 [Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220419-10:01:10,622 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0".
220419-10:01:10,635 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask".
220419-10:01:13,231 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
220419-10:01:13,308 nipype.workflow INFO:
	 [Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
220419-10:01:14,498 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
220419-10:01:15,285 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
220419-10:01:15,323 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220419-10:01:15,326 nipype.workflow INFO:
	 [Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220419-10:01:15,330 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220419-11:50:07,347 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
220419-11:50:13,190 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs1" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220419-11:50:13,273 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:13,277 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:13,282 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:13,551 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220419-11:50:13,687 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:13,708 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:13,712 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220419-11:50:50,537 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs1".
220419-11:50:57,26 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs0".
220419-11:51:01,512 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
220419-11:51:01,560 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220419-11:51:01,673 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:01,699 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-11:51:01,702 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:01,864 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs0".
220419-11:51:01,872 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs1" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220419-11:51:01,923 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:01,942 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-11:51:01,947 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:02,73 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs1".
220419-11:51:02,92 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
220419-11:51:07,32 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
220419-11:51:08,379 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:08,382 nipype.workflow INFO:
	 [Node] Running "cortribbon" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-11:51:08,386 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:51:08,590 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon".
220419-11:51:12,800 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats1" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220419-11:51:12,862 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:51:12,865 nipype.workflow INFO:
	 [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:51:12,869 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:51:15,439 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220419-11:51:15,580 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:51:15,583 nipype.workflow INFO:
	 [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:51:15,586 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220419-11:59:06,246 nipype.workflow INFO:
	 [Node] Finished "_parcstats1".
220419-11:59:08,869 nipype.workflow INFO:
	 [Node] Finished "_parcstats0".
220419-11:59:13,912 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
220419-11:59:14,35 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats0" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220419-11:59:14,195 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:59:14,199 nipype.workflow INFO:
	 [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-11:59:14,204 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:59:14,353 nipype.workflow INFO:
	 [Node] Finished "_parcstats0".
220419-11:59:14,362 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats1" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220419-11:59:14,485 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:59:14,502 nipype.workflow INFO:
	 [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220419-11:59:14,507 nipype.interface INFO:
	 recon-all complete : Not running
220419-11:59:14,628 nipype.workflow INFO:
	 [Node] Finished "_parcstats1".
220419-11:59:14,648 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
220419-11:59:19,592 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
220419-11:59:19,719 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220419-11:59:19,723 nipype.workflow INFO:
	 [Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220419-11:59:19,727 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220419-11:59:59,921 nipype.workflow WARNING:
	 Storing result file without outputs
220419-11:59:59,928 nipype.workflow WARNING:
	 [Node] Error on "smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" (/path/to/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB577_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3)
220419-12:00:00,612 nipype.workflow ERROR:
	 Node autorecon3 failed to run on host host-machine.
220419-12:00:00,618 nipype.workflow ERROR:
	 Saving crash info to /out/smriprep/sub-SUB577/log/20220419-093910_411669c1-a518-439f-b581-40175e148f47/crash-20220419-120000-pcamach2-autorecon3-ef2cb235-7a77-4bba-aceb-70df30898c91.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
    self.raise_exception(runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
    raise RuntimeError(
RuntimeError: Command:
recon-all -autorecon3 -openmp 8 -subjid sub-SUB577 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /opt/scratch/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
-rw-rw-r-- 1 pcamach2 redacted_redacted_access 422749 Apr 19 11:50 /opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.log
Linux redacted-redacted-14 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.local-copy'
#-----------------------------------------
#@# AParc-to-ASeg aparc Tue Apr 19 11:59:21 CDT 2022
/opt/scratch/freesurfer/sub-SUB577

 mri_aparc2aseg --s sub-SUB577 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

relabeling unlikely voxels interior to white matter surface:
	norm: mri/norm.mgz
	 XFORM: mri/transforms/talairach.m3z
	GCA: /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
	label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /opt/scratch/freesurfer
subject sub-SUB577
outvol /opt/scratch/freesurfer/sub-SUB577/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/lh.white

Reading lh pial surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/lh.pial

Loading lh annotations from /opt/scratch/freesurfer/sub-SUB577/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/rh.white

Reading rh pial surface 
 /opt/scratch/freesurfer/sub-SUB577/surf/rh.pial

Loading rh annotations from /opt/scratch/freesurfer/sub-SUB577/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /opt/scratch/freesurfer/sub-SUB577/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /opt/scratch/freesurfer/sub-SUB577/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mri_aparc2aseg: could not read mri/aseg.auto_noCCseg.label_intensities.txt
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
setting orig areas to linear transform determinant scaled 6.56
No such file or directory
Linux redacted-redacted-14 5.4.0-99-generic #112-Ubuntu SMP Thu Feb 3 13:50:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-SUB577 exited with ERRORS at Tue Apr 19 11:59:59 CDT 2022

For more details, see the log file /opt/scratch/freesurfer/sub-SUB577/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

220419-12:00:02,607 nipype.workflow ERROR:
	 could not run node: smriprep_wf.single_subject_SUB577_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3
Preprocessing did not finish successfully. Errors occurred while processing data from participants: SUB577 (1). Check the HTML reports for details.

from fastsurfer.

LeHenschel commented on July 29, 2024

Hey,

thanks for taking the time to checking the integration. The missing file is generated in mri_ca_label with FreeSurfer which we do not run (the segmentation is automatically generated with the DL-Net). I can check if we can generate it based on our segmentation. The aparc2aseg command might fail for FastSurfer later on, because we do not generate all surface annotations (aparc.a2009s will be missing), unless you run FastSurfer with the "--fsaparc" flag.

However, I am not sure, why you are running this step (aparc2aseg) in the first place. The file aparc.DKTatlas+aseg.mgz and aparc+aseg.mgz are generated by default with FreeSurfer 6.0 and should therefore already exist in a FreeSurfer processed directory. The same is true for FastSurfer (aparc.DKTatlas+aseg.mgz and aparc+aseg.mgz already exists). Is there any specific reason why this rerun is necessary? And do you need all three atlas segmentations (aparc+aseg.mgz, aparc.DKTatlas+aseg.mgz and aparc.a2009s+aseg.mgz)?

from fastsurfer.

pcamach2 commented on July 29, 2024

@LeHenschel thank you for the insight! From my understanding, the anatomical workflow in sMRIPrep recognizes that there is a pre-existing Freesurfer output and only runs commands that it needs to generate files that are not recognized as being present in that participant's Freesurfer (here using FastSurfer) directory. Perhaps this workflow is set to run because the nipype/sMRIPrep code is looking for these annotation files?

@effigies is there a workaround to prevent aparc2aseg if it is not necessary for sMRIPrep to run again after being given FastSurfer outputs as --fs-subjects-dir? Maybe adding an option to allow a less strict check of the directory contents when using FastSurfer would fix this bug?

from fastsurfer.

effigies commented on July 29, 2024

The "workaround" would be to touch any files you don't want sMRIPrep (more specifically, the Nipype ReconAll interface) to check are generated.

The fix would require a small Python function to distinguish FastSurfer- and FreeSurfer-reconstructed subjects. We could then simply detect the case at runtime and replace the entire FreeSurfer workflow with a minimal one that does not attempt reconstruction.

Once that is done, we would be in a good spot to actually include running FastSurfer and not just tolerate precomputed FastSurfer directories. This would require wrapping FastSurfer as a Nipype interface/workflow.

Apologies, I don't have much time to devote to this one at the moment, but I am happy to review pull requests or answer questions about the code to someone who can put in the effort. I can sketch out the workflows needed, but there will be some testing and fiddling to make sure everything works.

from fastsurfer.

pcamach2 commented on July 29, 2024

@effigies thank you! I would like to use this as part of my thesis work, so I will work on the code and keep you updated. Would it be alright to assign me to handle the issue I opened on the sMRIPrep repo nipreps/smriprep#278 ?

from fastsurfer.

pcamach2 commented on July 29, 2024

The fix of running touch on the mri/aseg.auto_noCCseg.label_intensities.txt file resolves the error and allows sMRIPrep to complete.

Run Command:

$ singularity run --nv -B ./bids:/data,./bids/derivatives:/out,/redacted/singularity_images/fslicense/license.txt:/opt/freesurfer/license.txt,./bids/derivatives/fastsurfer:/opt/scratch/freesurfer /redacted/singularity_images/smriprep/smriprep.sif /data/ /out/ --fs-subjects-dir /opt/scratch/freesurfer --fs-license-file /opt/freesurfer/license.txt participant --participant-label sub-SUB111

Terminal Output:

/opt/conda/lib/python3.8/site-packages/bids/layout/models.py:148: FutureWarning: The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
  warnings.warn("The 'extension' entity currently excludes the leading dot ('.'). "
220421-11:36:21,298 nipype.workflow Level 25:
	 
    Running sMRIPrep version 0.8.3:
      * BIDS dataset path: /data.
      * Participant list: ['SUB111'].
      * Run identifier: 20220421-113619_7dda58d4-ef6a-4a13-93e9-9ae653f0f175.

    Spatial References: <none>.
    
220421-11:36:21,756 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220421-11:36:30,291 nipype.workflow Level 25:
	 Works derived from this sMRIPrep execution should include the following boilerplate:


Results included in this manuscript come from preprocessing
performed using *sMRIPprep* 0.8.3
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.6.1
(@nipype1; @nipype2; RRID:SCR_002502).


Anatomical data preprocessing

: A total of 1 T1-weighted (T1w) images were found within the input
BIDS dataset.The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.3.3 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 6.0.5.1:57b01774, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].


For more details of the pipeline, see [the section corresponding
to workflows in *sMRIPrep*'s documentation](https://smriprep.readthedocs.io/en/latest/workflows.html "sMRIPrep's documentation").


### References


220421-11:36:37,661 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.full_wm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/full_wm".
220421-11:36:37,662 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_norm_wf/outputnode".
220421-11:36:37,950 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
220421-11:36:37,984 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
220421-11:36:38,140 nipype.workflow INFO:
	 [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
220421-11:36:38,387 nipype.workflow INFO:
	 [Node] Running "lap_tmpl" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1
220421-11:36:38,395 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_norm_wf.outputnode".
220421-11:36:38,428 nipype.workflow INFO:
	 [Node] Running "full_wm" ("nipype.interfaces.utility.wrappers.Function")
220421-11:36:38,501 nipype.workflow INFO:
	 [Node] Running "res_tmpl" ("niworkflows.interfaces.nibabel.RegridToZooms")
220421-11:36:39,880 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.full_wm".
220421-11:36:40,620 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.bidssrc" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/bidssrc".
220421-11:36:41,512 nipype.workflow INFO:
	 [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
220421-11:36:41,553 nipype.interface INFO:
	 No "t2w" images found for sub-<undefined>
220421-11:36:41,553 nipype.interface INFO:
	 No "flair" images found for sub-<undefined>
220421-11:36:41,553 nipype.interface INFO:
	 No "roi" images found for sub-<undefined>
220421-11:36:41,620 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.bidssrc".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220421-11:36:43,212 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
220421-11:36:44,549 nipype.utils WARNING:
	 A newer version (1.7.1) of nipy/nipype is available. You are using 1.6.1
220421-11:36:44,728 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.fs_isrunning" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/fs_isrunning".
220421-11:36:46,630 nipype.workflow INFO:
	 [Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
220421-11:36:46,809 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions".
220421-11:36:48,516 nipype.workflow INFO:
	 [Node] Running "fs_isrunning" ("nipype.interfaces.utility.wrappers.Function")
220421-11:36:48,618 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.fs_isrunning".
220421-11:36:48,684 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.t1w_conform" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_template_wf/t1w_conform".
220421-11:36:48,684 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
220421-11:36:48,831 nipype.workflow INFO:
	 [Node] Setting-up "_t1w_conform0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0".
220421-11:36:48,914 nipype.workflow INFO:
	 [Node] Running "_t1w_conform0" ("niworkflows.interfaces.images.Conform")
220421-11:36:49,49 nipype.workflow INFO:
	 [Node] Finished "_t1w_conform0".
220421-11:36:49,112 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.t1w_conform".
220421-11:36:49,164 nipype.workflow INFO:
	 [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function")
220421-11:36:49,280 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources".
220421-11:36:50,329 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.get1st" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_template_wf/get1st".
220421-11:36:50,804 nipype.workflow INFO:
	 [Node] Running "get1st" ("nipype.interfaces.utility.base.Select")
220421-11:36:51,195 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_template_wf.get1st".
220421-11:36:51,513 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl".
220421-11:36:54,209 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl".
220421-11:36:54,294 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fov_check".
220421-11:36:54,618 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/truncate_images".
220421-11:36:54,728 nipype.workflow INFO:
	 [Node] Setting-up "_truncate_images0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
220421-11:36:54,762 nipype.workflow INFO:
	 [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
220421-11:36:54,808 nipype.workflow INFO:
	 [Node] Running "_truncate_images0" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_maths.nii.gz TruncateImageIntensity /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz 0.01 0.999 256
220421-11:36:55,446 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.fov_check".
220421-11:36:56,285 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl".
220421-11:36:56,679 nipype.workflow INFO:
	 [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge")
220421-11:36:56,814 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl".
220421-11:36:59,48 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/recon_config".
220421-11:36:59,746 nipype.workflow INFO:
	 [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
220421-11:36:59,895 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.recon_config".
220421-11:37:03,936 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
220421-11:37:05,541 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon1 -noskullstrip -cw256 -hires -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -expert /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220421-11:37:05,545 nipype.workflow INFO:
	 [Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -noskullstrip -cw256 -hires -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -expert /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220421-11:37:05,604 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon1 -noskullstrip -cw256 -hires -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -expert /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts -nomotioncor -nonuintensitycor -nonormalization
220421-11:37:18,282 nipype.workflow INFO:
	 [Node] Finished "_truncate_images0".
220421-11:37:18,298 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.truncate_images".
220421-11:37:20,647 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4".
220421-11:37:20,729 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n40" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
220421-11:37:20,803 nipype.workflow INFO:
	 [Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-SUB111_ses-A_T1w_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-SUB111_ses-A_T1w_maths_corrected.nii.gz --shrink-factor 4
220421-11:38:45,98 nipype.workflow INFO:
	 [Node] Finished "_inu_n40".
220421-11:38:45,131 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.inu_n4".
220421-11:38:46,722 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/lap_target".
220421-11:38:46,764 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/res_target".
220421-11:38:46,996 nipype.workflow INFO:
	 [Node] Running "lap_target" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_maths_corrected_maths.nii.gz Laplacian /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB111_ses-A_T1w_maths_corrected.nii.gz 1.5 1
220421-11:38:47,299 nipype.workflow INFO:
	 [Node] Running "res_target" ("niworkflows.interfaces.nibabel.RegridToZooms")
220421-11:38:50,567 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.res_target".
220421-11:38:52,681 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/init_aff".
220421-11:38:52,859 nipype.workflow INFO:
	 [Node] Running "init_aff" ("nipype.interfaces.ants.utils.AI"), a CommandLine Interface with command:
antsAI -c [10,1e-06,10] -d 3 -x /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_regrid.nii.gz,/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-SUB111_ses-A_T1w_maths_corrected_regrid.nii.gz,32,Regular,0.25] -o initialization.mat -p 0 -s [15,0.1] -g [40.0,0x40x40] -t Affine[0.1] -v 1
220421-11:39:13,395 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.lap_target".
220421-11:39:14,437 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/mrg_target".
220421-11:39:14,757 nipype.workflow INFO:
	 [Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge")
220421-11:39:14,875 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.mrg_target".
220421-11:39:23,396 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.init_aff".
220421-11:39:24,866 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/norm".
220421-11:39:24,994 nipype.workflow INFO:
	 [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB111_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB111_ses-A_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-SUB111_ses-A_T1w_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-SUB111_ses-A_T1w_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ]  --write-composite-transform 0
220421-11:40:00,757 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
220421-11:40:06,777 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm".
220421-11:40:07,387 nipype.workflow INFO:
	 [Node] Running "fsnative2t1w_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /opt/scratch/freesurfer/sub-SUB111/mri/T1.mgz --dst /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz
220421-11:41:14,758 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm".
Captured warning (<class 'UserWarning'>): Reference space not set
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220421-11:41:20,817 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm".
220421-11:41:20,881 nipype.workflow INFO:
	 [Node] Running "t1w2fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --invert --outlta /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta
220421-11:41:21,182 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm".
220421-11:51:43,220 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.norm".
220421-11:51:45,593 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask".
220421-11:51:45,604 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask".
220421-11:51:45,729 nipype.workflow INFO:
	 [Node] Running "map_wmmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/full_wm/summap.nii.gz --interpolation Gaussian --output summap_trans.nii.gz --reference-image /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz --transform [ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220421-11:51:45,745 nipype.workflow INFO:
	 [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /home/pcamach2/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz --transform [ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz
220421-11:52:43,883 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask".
220421-11:52:45,255 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask".
220421-11:52:45,470 nipype.workflow INFO:
	 [Node] Running "thr_brainmask" ("nipype.interfaces.ants.utils.ThresholdImage"), a CommandLine Interface with command:
ThresholdImage 3 /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000
220421-11:52:49,183 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask".
220421-11:52:49,237 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.map_wmmask".
220421-11:52:51,318 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
220421-11:52:51,382 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final".
220421-11:52:51,443 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
220421-11:52:51,478 nipype.workflow INFO:
	 [Node] Running "dil_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2
220421-11:52:51,488 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
220421-11:52:51,669 nipype.workflow INFO:
	 [Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-SUB111_ses-A_T1w_corrected.nii.gz, sub-SUB111_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/map_wmmask/summap_trans.nii.gz
220421-11:52:51,695 nipype.workflow INFO:
	 [Node] Running "03_pad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10
220421-11:52:55,653 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.dil_brainmask".
220421-11:52:57,306 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask".
220421-11:52:57,491 nipype.workflow INFO:
	 [Node] Running "get_brainmask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220421-11:52:57,923 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask".
220421-11:53:01,358 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.get_brainmask".
220421-11:53:41,928 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0".
220421-11:53:41,959 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final".
220421-11:53:43,307 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/apply_mask".
220421-11:53:43,349 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos".
220421-11:53:43,369 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
220421-11:53:43,438 nipype.workflow INFO:
	 [Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220421-11:53:43,491 nipype.workflow INFO:
	 [Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command:
Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-SUB111_ses-A_T1w_corrected.nii.gz --likelihood-model Gaussian --mask-image /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-SUB111_ses-A_T1w_corrected_labeled.nii.gz,POSTERIOR_%02d.nii.gz] --use-random-seed 1
220421-11:53:46,61 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0".
220421-11:53:46,75 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.apply_mask".
220421-11:55:46,416 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos".
220421-11:55:47,473 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
220421-11:55:47,564 nipype.workflow INFO:
	 [Node] Running "02_pad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-SUB111_ses-A_T1w_corrected_labeled.nii.gz 10
220421-11:55:50,39 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm".
220421-11:55:59,905 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
220421-11:56:00,0 nipype.workflow INFO:
	 [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function")
220421-11:56:01,425 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels".
220421-11:56:01,914 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm".
220421-11:56:01,915 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf".
220421-11:56:01,916 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
220421-11:56:01,962 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm".
220421-11:56:01,965 nipype.workflow INFO:
	 [Node] Running "06_get_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02.nii.gz
220421-11:56:02,92 nipype.workflow INFO:
	 [Node] Running "05_get_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-03.nii.gz
220421-11:56:02,160 nipype.workflow INFO:
	 [Node] Running "27_depad_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz -10
220421-11:56:02,272 nipype.workflow INFO:
	 [Node] Running "10_me_csf" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz ME /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-01.nii.gz 10
220421-11:56:03,854 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf".
220421-11:56:04,20 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
220421-11:56:04,132 nipype.workflow INFO:
	 [Node] Running "apply_wm_prior" ("nipype.interfaces.utility.wrappers.Function")
220421-11:56:06,579 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_wm_prior".
220421-11:56:06,608 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm".
220421-11:56:07,689 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm".
220421-11:56:08,31 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
220421-11:56:08,33 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
220421-11:56:08,41 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final".
220421-11:56:08,72 nipype.workflow INFO:
	 [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz
220421-11:56:08,96 nipype.workflow INFO:
	 [Node] Setting-up "_inu_n4_final0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/inu_n4_final/mapflow/_inu_n4_final0".
220421-11:56:08,136 nipype.workflow INFO:
	 [Node] Running "07_fill_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz 2
220421-11:56:08,145 nipype.workflow INFO:
	 [Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-SUB111_ses-A_T1w_corrected.nii.gz, sub-SUB111_ses-A_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_wm_prior/prodmap.nii.gz
220421-11:56:10,465 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm".
220421-11:56:12,25 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
220421-11:56:12,66 nipype.workflow INFO:
	 [Node] Running "26_depad_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10
220421-11:56:14,241 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf".
220421-11:56:16,265 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm".
220421-11:56:36,455 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm".
220421-11:56:38,63 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
220421-11:56:38,149 nipype.workflow INFO:
	 [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02_maths.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz
220421-11:56:41,189 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm".
220421-11:56:42,67 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm".
220421-11:56:42,184 nipype.workflow INFO:
	 [Node] Running "11_add_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 08_mult_gm_maths.nii.gz addtozero /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-SUB111_ses-A_T1w_corrected_labeled_maths_class-01_maths.nii.gz
220421-11:56:52,935 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm".
220421-11:56:54,80 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
220421-11:56:54,123 nipype.workflow INFO:
	 [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz
220421-11:56:56,384 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm".
220421-11:56:58,81 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
220421-11:56:58,82 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
220421-11:56:58,144 nipype.workflow INFO:
	 [Node] Running "13_add_gm_wm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz
220421-11:56:58,167 nipype.workflow INFO:
	 [Node] Running "25_depad_gm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10
220421-11:56:59,5 nipype.workflow INFO:
	 [Node] Finished "_inu_n4_final0".
220421-11:56:59,17 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.inu_n4_final".
220421-11:57:00,577 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm".
220421-11:57:02,82 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms".
220421-11:57:02,166 nipype.workflow INFO:
	 [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge")
220421-11:57:02,216 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms".
220421-11:57:09,105 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm".
220421-11:57:10,102 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
220421-11:57:10,103 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
220421-11:57:10,136 nipype.workflow INFO:
	 [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function")
220421-11:57:10,205 nipype.workflow INFO:
	 [Node] Running "24_depad_segm" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10
220421-11:57:10,983 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2".
220421-11:57:12,98 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7".
220421-11:57:12,304 nipype.workflow INFO:
	 [Node] Running "15_add_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz
220421-11:57:12,591 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm".
220421-11:57:21,982 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7".
220421-11:57:22,110 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7".
220421-11:57:22,205 nipype.workflow INFO:
	 [Node] Running "16_me_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2
220421-11:57:30,952 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7".
220421-11:57:32,119 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7".
220421-11:57:32,276 nipype.workflow INFO:
	 [Node] Running "17_comp_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz
220421-11:57:37,157 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7".
220421-11:57:38,190 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7".
220421-11:57:38,332 nipype.workflow INFO:
	 [Node] Running "18_md_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4
220421-11:57:43,662 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7".
220421-11:57:44,129 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7".
220421-11:57:44,214 nipype.workflow INFO:
	 [Node] Running "19_fill_7" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2
220421-11:58:09,345 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7".
220421-11:58:10,153 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
220421-11:58:10,242 nipype.workflow INFO:
	 [Node] Running "20_add_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
220421-11:58:20,533 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2".
220421-11:58:22,187 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
220421-11:58:22,319 nipype.workflow INFO:
	 [Node] Running "21_md_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5
220421-11:58:29,723 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2".
220421-11:58:30,173 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
220421-11:58:30,235 nipype.workflow INFO:
	 [Node] Running "22_me_7_2" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5
220421-11:58:38,669 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2".
220421-11:58:40,218 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
220421-11:58:40,262 nipype.workflow INFO:
	 [Node] Running "23_depad_mask" ("nipype.interfaces.ants.utils.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10
220421-11:58:42,226 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask".
220421-11:58:44,186 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform".
220421-11:58:44,221 nipype.workflow INFO:
	 [Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function")
220421-11:58:44,987 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform".
220421-11:59:03,472 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask".
Captured warning (<class 'FutureWarning'>): The 'extension' entity currently excludes the leading dot ('.'). As of version 0.14.0, it will include the leading dot. To suppress this warning and include the leading dot, use `bids.config.set_option('extension_initial_dot', True)`.
220421-11:59:03,496 nipype.workflow INFO:
	 [Node] Setting-up "_apply_mask0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/apply_mask/mapflow/_apply_mask0".
220421-11:59:03,538 nipype.workflow INFO:
	 [Node] Running "_apply_mask0" ("niworkflows.interfaces.nibabel.ApplyMask")
220421-11:59:05,484 nipype.workflow INFO:
	 [Node] Finished "_apply_mask0".
220421-11:59:05,498 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.apply_mask".
220421-11:59:13,871 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
220421-11:59:14,462 nipype.workflow INFO:
	 [Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
220421-11:59:20,381 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
220421-11:59:21,393 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
220421-11:59:21,551 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220421-11:59:21,556 nipype.workflow INFO:
	 [Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220421-11:59:21,559 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nogcareg -nocanorm -nocalabel -nonormalization2 -nomaskbfs -nosegmentation -nofill
220421-14:13:56,480 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
220421-14:14:03,62 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220421-14:14:03,133 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:03,137 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:03,141 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:03,183 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220421-14:14:03,273 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:03,278 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:03,283 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nopial -nocortparc3 -nopctsurfcon
220421-14:14:46,158 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs0".
220421-14:14:46,352 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs1".
220421-14:14:47,762 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
220421-14:14:47,814 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
220421-14:14:47,881 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:47,925 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220421-14:14:47,930 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:48,79 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs0".
220421-14:14:48,86 nipype.workflow INFO:
	 [Node] Setting-up "_autorecon_surfs1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
220421-14:14:48,160 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:48,164 nipype.workflow INFO:
	 [Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220421-14:14:48,168 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:48,314 nipype.workflow INFO:
	 [Node] Finished "_autorecon_surfs1".
220421-14:14:48,336 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
220421-14:14:49,757 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
220421-14:14:49,829 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:49,850 nipype.workflow INFO:
	 [Node] Running "cortribbon" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220421-14:14:49,855 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:14:50,40 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon".
220421-14:14:54,328 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220421-14:14:54,392 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:14:54,425 nipype.workflow INFO:
	 [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:14:54,430 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:14:57,94 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220421-14:14:57,134 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:14:57,138 nipype.workflow INFO:
	 [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:14:57,141 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
220421-14:23:22,173 nipype.workflow INFO:
	 [Node] Finished "_parcstats0".
220421-14:23:28,118 nipype.workflow INFO:
	 [Node] Finished "_parcstats1".
220421-14:23:31,553 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
220421-14:23:31,615 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
220421-14:23:31,715 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:23:31,719 nipype.workflow INFO:
	 [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220421-14:23:31,723 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:23:31,890 nipype.workflow INFO:
	 [Node] Finished "_parcstats0".
220421-14:23:31,899 nipype.workflow INFO:
	 [Node] Setting-up "_parcstats1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
220421-14:23:31,959 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:23:31,962 nipype.workflow INFO:
	 [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
220421-14:23:31,967 nipype.interface INFO:
	 recon-all complete : Not running
220421-14:23:32,121 nipype.workflow INFO:
	 [Node] Finished "_parcstats1".
220421-14:23:32,156 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
220421-14:23:35,556 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
220421-14:23:35,647 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220421-14:23:35,651 nipype.workflow INFO:
	 [Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220421-14:23:35,656 nipype.interface INFO:
	 resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-SUB111 -sd /opt/scratch/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nobalabels
220421-14:46:35,352 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3".
220421-14:46:35,741 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces".
220421-14:46:35,743 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource".
220421-14:46:35,744 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
220421-14:46:35,900 nipype.workflow INFO:
	 [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
220421-14:46:36,41 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource".
220421-14:46:37,214 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_reports_wf/recon_report".
220421-14:46:37,239 nipype.workflow INFO:
	 [Node] Running "recon_report" ("smriprep.interfaces.reports.FSSurfaceReport")
220421-14:46:37,849 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.resample" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample".
/opt/conda/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "
220421-14:46:39,94 nipype.workflow INFO:
	 [Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource")
220421-14:46:39,147 nipype.workflow INFO:
	 [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
220421-14:46:39,149 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces".
220421-14:46:39,221 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource".
220421-14:46:39,870 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.resample" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/resample".
220421-14:46:41,538 nipype.workflow INFO:
	 [Node] Running "resample" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --interp nearest --lta /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/resample/aseg.mgz --targ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-SUB111_ses-A_T1w_corrected_xform.nii.gz --o seg.nii.gz
220421-14:46:42,166 nipype.workflow INFO:
	 [Node] Running "resample" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --interp nearest --lta /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample/aparc+aseg.mgz --targ /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-SUB111_ses-A_T1w_corrected_xform.nii.gz --o seg.nii.gz
220421-14:46:45,709 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
220421-14:46:45,794 nipype.workflow INFO:
	 [Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.smoothwm 0.5 midthickness
220421-14:46:45,874 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
220421-14:46:45,982 nipype.workflow INFO:
	 [Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.pial -thickness -thickness_name /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.thickness /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.smoothwm 0.5 midthickness
220421-14:46:46,822 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.resample".
220421-14:46:47,467 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.resample".
220421-14:46:47,838 nipype.interface WARNING:
	 Changing /out/smriprep/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_desc-aseg_dseg.nii.gz dtype from float32 to int16
220421-14:46:51,436 nipype.interface WARNING:
	 Changing /out/smriprep/sub-SUB111/ses-A/anat/sub-SUB111_ses-A_desc-aparcaseg_dseg.nii.gz dtype from float32 to int16
220421-14:46:51,631 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.refine" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/refine".
220421-14:46:51,672 nipype.workflow INFO:
	 [Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask")
220421-14:47:06,953 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_reports_wf.recon_report".
220421-14:48:55,417 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.refine".
220421-14:48:56,459 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.applyrefined" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/applyrefined".
220421-14:49:00,102 nipype.workflow INFO:
	 [Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-SUB111_ses-A_T1w_corrected_xform.nii.gz -mas /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/refine/sub-SUB111_ses-A_T1w_corrected_xform_rbrainmask.nii.gz /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/applyrefined/sub-SUB111_ses-A_T1w_corrected_xform_masked.nii.gz
220421-14:49:03,525 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.applyrefined".
220421-14:49:04,451 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.t1w_dseg" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/t1w_dseg".
220421-14:49:04,536 nipype.workflow INFO:
	 [Node] Running "t1w_dseg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -N -p -g -S 1 /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/t1w_dseg/sub-SUB111_ses-A_T1w_corrected_xform_masked.nii.gz
220421-14:54:08,592 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.t1w_dseg".
220421-14:54:10,649 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.lut_t1w_dseg" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/lut_t1w_dseg".
220421-14:54:10,837 nipype.workflow INFO:
	 [Node] Running "lut_t1w_dseg" ("nipype.interfaces.utility.wrappers.Function")
220421-14:54:11,844 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.lut_t1w_dseg".
220421-14:54:13,951 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_reports_wf.seg_rpt" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/anat_reports_wf/seg_rpt".
220421-14:54:16,474 nipype.workflow INFO:
	 [Node] Running "seg_rpt" ("niworkflows.interfaces.reportlets.masks.ROIsPlot")
/opt/conda/lib/python3.8/site-packages/nilearn/datasets/__init__.py:93: FutureWarning: Fetchers from the nilearn.datasets module will be updated in version 0.9 to return python strings instead of bytes and Pandas dataframes instead of Numpy arrays.
  warn("Fetchers from the nilearn.datasets module will be "
220421-14:55:06,270 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.anat_reports_wf.seg_rpt".
220421-15:05:01,617 nipype.workflow INFO:
	 [Node] Finished "_midthickness1".
220421-15:05:01,693 nipype.workflow INFO:
	 [Node] Finished "_midthickness0".
220421-15:05:07,722 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness".
220421-15:05:07,764 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
220421-15:05:07,771 nipype.workflow INFO:
	 [Node] Cached "_midthickness0" - collecting precomputed outputs
220421-15:05:07,771 nipype.workflow INFO:
	 [Node] "_midthickness0" found cached.
220421-15:05:07,774 nipype.workflow INFO:
	 [Node] Setting-up "_midthickness1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
220421-15:05:07,780 nipype.workflow INFO:
	 [Node] Cached "_midthickness1" - collecting precomputed outputs
220421-15:05:07,780 nipype.workflow INFO:
	 [Node] "_midthickness1" found cached.
220421-15:05:07,795 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness".
220421-15:05:09,404 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness".
220421-15:05:09,473 nipype.workflow INFO:
	 [Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
220421-15:05:09,847 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
220421-15:05:15,408 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
220421-15:05:15,409 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
220421-15:05:15,412 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
220421-15:05:15,417 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
220421-15:05:15,420 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
220421-15:05:15,423 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
220421-15:05:15,426 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii6" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
220421-15:05:15,430 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
220421-15:05:15,471 nipype.workflow INFO:
	 [Node] Running "_fs2gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/rh.pial /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3/rh.pial_converted.gii
220421-15:05:15,472 nipype.workflow INFO:
	 [Node] Running "_fs2gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/lh.smoothwm /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1/lh.smoothwm_converted.gii
220421-15:05:15,513 nipype.workflow INFO:
	 [Node] Running "_fs2gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/lh.pial /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2/lh.pial_converted.gii
220421-15:05:15,520 nipype.workflow INFO:
	 [Node] Running "_fs2gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/lh.inflated /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5/lh.inflated_converted.gii
220421-15:05:15,538 nipype.workflow INFO:
	 [Node] Running "_fs2gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/rh.midthickness /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6/rh.midthickness_converted.gii
220421-15:05:15,540 nipype.workflow INFO:
	 [Node] Running "_fs2gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/lh.midthickness /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7/lh.midthickness_converted.gii
220421-15:05:15,592 nipype.workflow INFO:
	 [Node] Running "_fs2gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/rh.smoothwm /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0/rh.smoothwm_converted.gii
220421-15:05:15,630 nipype.workflow INFO:
	 [Node] Running "_fs2gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /opt/scratch/freesurfer/sub-SUB111/surf/rh.inflated /redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4/rh.inflated_converted.gii
220421-15:05:18,223 nipype.workflow INFO:
	 [Node] Finished "_fs2gii7".
220421-15:05:18,306 nipype.workflow INFO:
	 [Node] Finished "_fs2gii6".
220421-15:05:18,352 nipype.workflow INFO:
	 [Node] Finished "_fs2gii5".
220421-15:05:18,374 nipype.workflow INFO:
	 [Node] Finished "_fs2gii1".
220421-15:05:18,399 nipype.workflow INFO:
	 [Node] Finished "_fs2gii0".
220421-15:05:18,402 nipype.workflow INFO:
	 [Node] Finished "_fs2gii2".
220421-15:05:18,641 nipype.workflow INFO:
	 [Node] Finished "_fs2gii4".
220421-15:05:24,431 nipype.workflow INFO:
	 [Node] Finished "_fs2gii3".
220421-15:05:25,425 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii".
220421-15:05:25,504 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
220421-15:05:25,510 nipype.workflow INFO:
	 [Node] Cached "_fs2gii0" - collecting precomputed outputs
220421-15:05:25,510 nipype.workflow INFO:
	 [Node] "_fs2gii0" found cached.
220421-15:05:25,513 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
220421-15:05:25,519 nipype.workflow INFO:
	 [Node] Cached "_fs2gii1" - collecting precomputed outputs
220421-15:05:25,519 nipype.workflow INFO:
	 [Node] "_fs2gii1" found cached.
220421-15:05:25,522 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
220421-15:05:25,527 nipype.workflow INFO:
	 [Node] Cached "_fs2gii2" - collecting precomputed outputs
220421-15:05:25,527 nipype.workflow INFO:
	 [Node] "_fs2gii2" found cached.
220421-15:05:25,529 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii3" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
220421-15:05:25,536 nipype.workflow INFO:
	 [Node] Cached "_fs2gii3" - collecting precomputed outputs
220421-15:05:25,536 nipype.workflow INFO:
	 [Node] "_fs2gii3" found cached.
220421-15:05:25,539 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii4" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
220421-15:05:25,544 nipype.workflow INFO:
	 [Node] Cached "_fs2gii4" - collecting precomputed outputs
220421-15:05:25,545 nipype.workflow INFO:
	 [Node] "_fs2gii4" found cached.
220421-15:05:25,547 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii5" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
220421-15:05:25,552 nipype.workflow INFO:
	 [Node] Cached "_fs2gii5" - collecting precomputed outputs
220421-15:05:25,553 nipype.workflow INFO:
	 [Node] "_fs2gii5" found cached.
220421-15:05:25,556 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii6" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
220421-15:05:25,563 nipype.workflow INFO:
	 [Node] Cached "_fs2gii6" - collecting precomputed outputs
220421-15:05:25,563 nipype.workflow INFO:
	 [Node] "_fs2gii6" found cached.
220421-15:05:25,566 nipype.workflow INFO:
	 [Node] Setting-up "_fs2gii7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
220421-15:05:25,572 nipype.workflow INFO:
	 [Node] Cached "_fs2gii7" - collecting precomputed outputs
220421-15:05:25,572 nipype.workflow INFO:
	 [Node] "_fs2gii7" found cached.
220421-15:05:25,633 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii".
220421-15:05:29,434 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
220421-15:05:29,437 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
220421-15:05:29,439 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
220421-15:05:29,439 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
220421-15:05:29,440 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
220421-15:05:29,441 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
220421-15:05:29,441 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
220421-15:05:29,443 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs6" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
220421-15:05:29,478 nipype.workflow INFO:
	 [Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,479 nipype.workflow INFO:
	 [Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,482 nipype.workflow INFO:
	 [Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,487 nipype.workflow INFO:
	 [Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,498 nipype.workflow INFO:
	 [Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,500 nipype.workflow INFO:
	 [Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,511 nipype.workflow INFO:
	 [Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:29,517 nipype.workflow INFO:
	 [Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf")
220421-15:05:30,489 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs2".
220421-15:05:30,594 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs3".
220421-15:05:30,605 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs5".
220421-15:05:30,618 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs1".
220421-15:05:30,651 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs0".
220421-15:05:32,364 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs7".
220421-15:05:33,820 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs4".
220421-15:05:38,691 nipype.workflow INFO:
	 [Node] Finished "_fix_surfs6".
220421-15:05:39,523 nipype.workflow INFO:
	 [Node] Setting-up "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs".
220421-15:05:39,552 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs0" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
220421-15:05:39,558 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs0" - collecting precomputed outputs
220421-15:05:39,559 nipype.workflow INFO:
	 [Node] "_fix_surfs0" found cached.
220421-15:05:39,561 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs1" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
220421-15:05:39,566 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs1" - collecting precomputed outputs
220421-15:05:39,566 nipype.workflow INFO:
	 [Node] "_fix_surfs1" found cached.
220421-15:05:39,568 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs2" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
220421-15:05:39,573 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs2" - collecting precomputed outputs
220421-15:05:39,574 nipype.workflow INFO:
	 [Node] "_fix_surfs2" found cached.
220421-15:05:39,576 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs3" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
220421-15:05:39,581 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs3" - collecting precomputed outputs
220421-15:05:39,581 nipype.workflow INFO:
	 [Node] "_fix_surfs3" found cached.
220421-15:05:39,584 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs4" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
220421-15:05:39,589 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs4" - collecting precomputed outputs
220421-15:05:39,589 nipype.workflow INFO:
	 [Node] "_fix_surfs4" found cached.
220421-15:05:39,592 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs5" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
220421-15:05:39,598 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs5" - collecting precomputed outputs
220421-15:05:39,598 nipype.workflow INFO:
	 [Node] "_fix_surfs5" found cached.
220421-15:05:39,600 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs6" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
220421-15:05:39,605 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs6" - collecting precomputed outputs
220421-15:05:39,605 nipype.workflow INFO:
	 [Node] "_fix_surfs6" found cached.
220421-15:05:39,607 nipype.workflow INFO:
	 [Node] Setting-up "_fix_surfs7" in "/redacted/pcamach2/SUB/beta/testing/SUB/work/smriprep_wf/single_subject_SUB111_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
220421-15:05:39,612 nipype.workflow INFO:
	 [Node] Cached "_fix_surfs7" - collecting precomputed outputs
220421-15:05:39,612 nipype.workflow INFO:
	 [Node] "_fix_surfs7" found cached.
220421-15:05:39,670 nipype.workflow INFO:
	 [Node] Finished "smriprep_wf.single_subject_SUB111_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs".

Thank you!

from fastsurfer.

m-reuter commented on July 29, 2024

I think this is currently working. May need to be revisited when we change anything major (like different names for files). Happy to re-open when necessary.

from fastsurfer.

Integrate with fmriprep about fastsurfer HOT 23 CLOSED

Comments (23)

Related Issues (20)

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent