scilus / tractoflow

TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity

TractoFlow pipeline

The TractoFlow pipeline is a fully automated and reproducible dMRI processing pipeline. TractoFlow takes raw DWI, b-values, b-vectors, T1 weighted image (and a reversed phase encoded b=0 if available) to process DTI, fODF metrics and a whole brain tractogram.

Documentation:

TractoFlow documentation is available here:

https://tractoflow-documentation.readthedocs.io

This documentation presents how to install and launch TractoFlow on a local computer and a High Performance Computer.

If you are a user and NOT A DEVELOPER, we HIGHLY RECOMMEND following the instructions on the documentation website.

Support:

For questions or help on TractoFlow, please create a topic on Neurostars with the tractoflow tag.

Before posting, please check the topics already created.

Singularity

If you are on Linux, we recommend using the Singularity container to run TractoFlow

Prebuild Singularity images are available here:

https://scil.usherbrooke.ca/pages/containers/

FOR DEVELOPERS: The containers repository is available here: containers-scilus

Docker

If you are on MacOS or Windows, we recommend using the Docker container to run TractoFlow

Prebuilt Docker images are available here:

https://hub.docker.com/r/scilus/scilus

FOR DEVELOPERS: The containers repository is available here: containers-scilus

Steps

Diffusion processes

• preliminary DWI brain extraction (FSL)
• denoise DWI (Mrtrix3)
• gibbs correction (Mrtrix3)
• topup (FSL)
• eddy (FSL)
• extract B0 (Scilpy)
• dwi brain extraction (FSL)
• N4 DWI (ANTs)
• crop DWI (Scilpy)
• upsample DWI (Scilpy)
• upsample B0 (Scilpy)
• extract SH fitted to DWI (Scilpy)

T1 processes

• denoise T1 (Scilpy)
• N4 T1 (ANTs)
• resample T1 (Scilpy)
• T1 brain extraction (ANTs)
• crop T1 (Scilpy)
• registration on diffusion (ANTs)
• tissue segmentation (FSL)

Metrics processes

• extract DTI shells (configurable in nextflow.config) (Scilpy)
• dti metrics (Scilpy)
• extract fODF shells (configurable in nextflow.config) (Scilpy)
• compute fiber response function (Scilpy)
• mean fiber response function (Scilpy)
• fODF and fODF-derived metrics (Scilpy)
• particle filter tractography maps (Scilpy)
• seeding mask (Scilpy)
• particle filter tracking (Scilpy)

Usage

See USAGE or run nextflow run main.nf --help

References

To refer to TractoFlow, please see References section on TractoFlow documentation

tractoflow's Issues

Unable to build from singularity img file

Hello

Seek help with installing tractoflow.

Please find the installation error log below.

(base) amitjc@AMiT:~/singularity/singularity$ singularity build singularity_tractoflow_2.0.0_8b39aee_2019-04-26.img singularity_tractoflow.def
FATAL: Unable to build from singularity_tractoflow.def: unable to open file singularity_tractoflow.def: open singularity_tractoflow.def: no such file or directory

Please Advice.

Thank you.

Best Regards,
Amit.

hardlinks instead of symlinks for the results folder

The work directory should not be removed, because of symlinks but may take up a lot of space.

One solution could be to use hardlinks and add the directive on how to do it in the documentation.

Is it a good idea or deleting the work folder is really bad practice?

broken bet prelim b0

first mean_b0 is broken with values outside the int16 range.

Dataset where I saw this: Alberta300

[ENH] Output BIDS like

-> sub-001/ses-1/

feature request: gradunwarp

Are there any plans to include https://github.com/Washington-University/gradunwarp to the pipeline?
It would help using the pipeline on data acquired with the HCP acquisition scheme.
Thanks!

Mean FRF computed if Set FRF is set

The Mean FRF is computed even if the set_frf option is enabled. We must to correct the when condition in the mean FRF process.

Multiple reverse b0 not supported

While processing a dataset I realize that rev_b0 can contain multiple volume (100x100x68x6) and it seems the scripts scil_prepare_topup_command.py does not support it. Well in fact nothing crash and topup takes a lot more time than usual without a visible improvement of results.

If this is the expected behavior, documentation should be adjusted in consequence.
If not, the script scil_prepare_topup_command.py should crash

T1 Alignment Recommended?

Hi Tractoflow team,

Quick question: Should T1 files be ACPC aligned (or subject to any other alignment) before being put into Tractoflow? Also, should the x-gradient in the bvecs be flipped for data coming from Siemens scanners (this is recommended for other softwares like AFQ). Congrats on the NeuroImage publication!

Thanks,
Steven

Tractoflow pipeline error “Read Bids”

Hello,
I am trying to launch the tractoflow pipeline on a example dataset (https://openneuro.org/datasets/ds003047/versions/1.0.0 1) on a linux system.
When I launch the pipeline I get an error with the “Read_BIDS” :
/Tractoflow [512] > ./nextflow run tractoflow/main.nf --bids /home/giacomo.garone/Tractoflow/DATA/ds003047-download --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity /home/giacomo.garone/Tractoflow/tractoflow_2.2.1_b9a527_2021-04-13.sif -resume
N E X T F L O W ~ version 19.04.0
Launching tractoflow/main.nf [pensive_jones] - revision: f66d0cdd95
TractoFlow pipeline
Start time: Fri Jul 23 17:22:05 CEST 2021
Input BIDS: /home/giacomo.garone/Tractoflow/DATA/ds003047-download
Clean_bids: false
executor > local (8)
[03/751dc8] process > Read_BIDS [100%] 4 of 4, failed: 4 ✘
[e8/6d6713] process > README [100%] 4 of 4, failed: 4
Pipeline completed at: Fri Jul 23 17:22:13 CEST 2021
Execution status: failed
Execution duration: 7.7s
[21/c99155] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (255) – Execution is retried (1)
[92/cab5cc] NOTE: Process README (README) terminated with an error exit status (255) – Execution is retried (1)
[b5/61dbb3] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (255) – Execution is retried (2)
[1b/1b259d] NOTE: Process README (README) terminated with an error exit status (255) – Execution is retried (2)
[46/13a5dc] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (255) – Execution is retried (3)
[22/ab40bf] NOTE: Process README (README) terminated with an error exit status (255) – Execution is retried (3)
WARN: Killing pending tasks (1)
ERROR ~ Error executing process > ‘Read_BIDS (Read_BIDS)’
Caused by:
Process Read_BIDS (Read_BIDS) terminated with an error exit status (255)
Command executed:
scil_validate_bids.py ds003047-download tractoflow_bids_struct.json --readout 0.062
Command exit status:
255
Command output:
(empty)
Command error:
FATAL: container creation failed: mount /proc/self/fd/10->/usr/local/var/singularity/mnt/session/rootfs error: can’t mount image /proc/self/fd/10: failed to mount squashfs filesystem: invalid argument
Work dir:
/home/giacomo.garone/Tractoflow/work/03/751dc885216a34b64c8d291552c3a4
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
– Check ‘.nextflow.log’ file for details

Can someone help me ?
Thank you very much in advance for your help !
Best
Giacomo

Remove invalid streamlines in tracking processes

Add scil_remove_invalid_streamlines.py in PFT and local tracking processes.

Updated Docker image?

Hello, just a friendly reminder asking you to update the Docker image to the latest version (2.3.0). Thanks for this awesome piece of software!

format of --manual_frf input

The USAGE --help of --manual_frf is not crystal clear and different than the behavior of options such as --dti_shells "0 1000".
--manual_frf sould not be used with "15 4 4" for example. It needs to be 15,4,4

Some users had errors with that.

Seeding Masks Failing

Hi Tractoflow team,

I am encountering an error when running Tractoflow with default parameters (besides turning Eddy correction off). I am running version 2.1.0 on a Linux HPC. Everything proceeds fine until reaching the Seeding Masks phase. I notice in the Slurm out file, that for every subject that enters the task, there are reports of 4 failures. For example, below are the last three lines from the process I am running currently:

[cd/a2a9fd] process > Segment_Tissues [100%] 4 of 4
[03/949a05] process > PFT_Maps [100%] 4 of 4
[e4/d0873c] process > Seeding_Mask [100%] 16 of 16, failed: 16

I had a similar error in a previous version of Tractoflow when running Eddy without specifying a singularity config file, but the changelog suggests config files are not needed anymore. Please let me know if you would need any more information to diagnose the issue.

Thanks,
Steven

Run Topup, but not Eddy; How to deal with different acquisition parameters.

Hi Tractoflow team,

I do QC with DTIPrep, which does Eddy + motion correction as well as automated volume removal, before using Tractoflow. Therefore, I do not need to do Eddy and motion again so I set --run_eddy false. However, DTIPrep does not do Topup, and some of my datasets have reverse b0 images. In the Slurm outfile, it looks like Eddy and Topup are one process (called Eddy). Is it possible to only run topup, or should I run topup before using Tractoflow?

Similarly, in this dataset there are some subjects who have reverse-encoded b0 and some who do not. What would be your suggested way of dealing with this? My main concern is that ideally all subjects would be considered in the mean FRF.

Thank you,
Steven

Fa tracking/seeding mask has wrong datatype

mrcalc $fa $params.pft_fa_seeding_mask_theshold -ge ${sid}__pft_seeding_mask.nii.gz
(Same for local) requires -datatype as uint8
Or use scil_image_math.py convert --data_type

This makes the pipeline crash at tracking.
OSError: The image me_s0__local_tracking_mask.nii.gz cannot be loaded as mask because its type <class 'numpy.float32'> is not compatible with a mask

Fix scil_image_math.py in Topup process.

Add --data_type float32 in scil_image_math.py otherwise if the rev_b0 is in int the script crash.

Remote Resource not found

Hi Tractoflow team,
I am attempting to run your pipeline on some OASIS DWI data on a CentOS HPC running SLURM.

I have successfully built a tractoflow image, and the HPC team has added singularity 3.6.0 and Nextflow 20.04.1 to the modules.

Upon running, I recieve the following error:

N E X T F L O W ~ version 20.04.1
Pulling nextflow-io/tractoflow …
Remote resource not found: https://api.github.com/repos/nextflow-io/tractoflow/contents/main.nf

I have downloaded the main.nf and nextflow.config from your repo, but to no avail.

Any ideas?

Topup: mean_b0 might already exist

The Topup process may crash if a reverse diff image is provided.

In main.nf:657

scil_image_math.py mean ${sid}__concatenated_rev_b0.nii.gz ${sid}__rev_b0_mean.nii.gz should have the -f flag.

[BUG] hcp 7t

No b0 found during Normalize_DWI process.
MRtrix dwinormalise fail :

Command:  dwiextract 100610__dwi_cropped.nii.gz -fslgrad 100610_dwi.bvec 100610_dwi.bval -bzero - | mrmath - mean - -axis 3 | mrstats - -mask fa_masked.nii.gz -output median

dwinormalise: [ERROR] dwiextract 100610__dwi_cropped.nii.gz -fslgrad 100610_dwi.bvec 100610_dwi.bval -bzero - | mrmath - mean - -axis 3 | mrstats - -mask fa_masked.nii.gz -output median (individual.py:66)
dwinormalise: [ERROR] Information from failed command:
dwinormalise:
              dwiextract: uncompressing image "100610__dwi_cropped.nii.gz"... [==================================================]
              dwiextract: [ERROR] No b=0 volumes present
              mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
              mrmath: [ERROR] error opening image "-"
              mrstats: [ERROR] no filename supplied to standard input (broken pipe?)
              mrstats: [ERROR] error opening image "-"

Eddy Process error exit status (134)

Hi Tractoflow team,
Do you possibly have a reference for the error codes that are produced by Tractoflow?

I have encountered the following error: Eddy (sub-OAS30125_ses-d0201) terminated with an error exit status (134) -- Execution is retried (3)

Possible skip

• Very small efficiency enhancement: If all first steps are false (--run_dwi_denoising false --run_eddy false --run_topup false + default false for gibbs correction), then Bet_Prelim can be skipped!

Streamline analysis and connectivity

Hi,

Once the TractoFlow pipeline is finished, i.e. tracking is finished, one has a .trk file of whole brain streamline. But which way could you recommend us to continue with:

1. Visualization of tractography superposed onto anatomical image?
2. Streamline analysis and connectivity? (tools, methods available, ...)

Multiple b0, personalization topup and T1 registration

Hello,

Thanks for this nice pipeline. I have some questions firstly regarding the use of multiple b0 in the pipeline and secondly about the personalization of both topup and T1 registration.

1. I used some data from Penthera3T in order to assess the pipeline, where 7 b0 were present in the dwi.nii.gz file. How does the pipeline deal with these several b0? Is an average of these 7 b0 computed at the beginning of the pipeline? If this is the case, are the 7 b0 realigned before computing the mean?

2. In my dataset I have only 1 b0 in the dwi.nii.gz file. In order to correct distorsions I have separately a set of 9 b0 in both AP and PA directions (computing mean from them to avoid noise of a unique b0 in the dwi.nii.gz). Then, I use both of them to estimate deformation field based on the mean b0 in AP and PA, then apply the distorsion correction on the dwi.nii.gz (having registered first the 9 b0 AP onto the unique b0 in the dwi.nii.gz file). How could I introduce this specific use of topup in the pipeline?

3. To register b0 onto T1, I use several registration from b0 to T2*, then to T2 and finally to T1. How could I introduce this specific registration in the pipeline?

Thanks for your time and advice.

Best,
Matthieu

[ENH] Improve Tractoflow while thinking about the QC

Each step of tractoflow needs to contains in some ways everything needed to QC it with before/after gifs + mean within mask.

Error Due to Default local_batch_size_gpu Setting in Non-GPU Environments

Hello,
I have completed testing the updated version and noticed that the default setting for local_batch_size_gpu is 10000. This configuration leads to an error when the GPU is not utilized (please refer to the attached screenshot for details). To prevent this issue, I suggest modifying the nextflow.config file to set local_batch_size_gpu to 0.

Breaking after SH fitting

Hello,

I'm trying to analyze a large dataset that contains scans from different manufacturers. I'm thinking of using an approach where the residuals from the SH fitting are analyzed. Would it be possible to insert a flag to tell tractoflow to stop after this fitting and not proceed with CSD?

Nexflow error

HI, I get an error running tractoflow on UBuntu 22.04 Jammy after installing Netflow successfully:

sudo nextflow run tractoflow -r 2.4.2
gives:

Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier

Any ideas how to solve this issue?

Customising a run of Tractoflow with lesion dataset

I have a dataset of patients with brain tumours and following recommendations from the SCIL paper: https://link.springer.com/chapter/10.1007/978-3-030-00931-1_43 I have created edema corrected tissue segmentations for PFT tractography. I would like to use these maps instead of the default outputs from FAST in tractoflow.

I have tried to do this by copying my new tissue segmentations into the respective subdirectories of the work folder for a previous run of TF (renamed according to TF conventions) but when running TF again with --resume option it doesn;t seem to recognise this and re-runs the segmentation along with many other steps of the diffusion preprocessing- which it had already done previouslyx

Is there any way to do this? Thanks.

Tractoflow does not support multi shell multi tissue CSD (MSMT-CSD)

Tractoflow pipeline does not support multi-shell multi-tissue CSD (MSMT-CSD). Only single shell single tissue (SSST-CSD) has been implemented even though scil_compute_msmt_fodf.py and scil_compute_msmt_frf.py exist.

A solution is to add an option in Tractoflow to use either the single shell fODF* or MSMT version.

An alternative solution would be to implement a new Nextflow pipeline for computing MSMT-fODF from Tractoflow ouptuts (similar to freewater_flow or NODDI_flow). However, the new pipeline would only improve fODF metrics (ex. for tractometry) but not the tractography!

*Multi shell CSD is actually already supported in Tractoflow. However, Tractoflow only estimates (user can also manually enter) a single FRF for all shells thus it can apply SSST-CSD.

EDDY Not Running, Finds an Incorrect Number of Subjects?

Hello,

I am testing tractoflow (Linux HPC, singularity container) on four subjects, with the input structure properly formatted. I ran the command, and I get an error for the EDDY process in the slurm outfile saying that 16 of 16 failed (which seems odd since I am only running 4 subjects). The DWI tasks before EDDY each showed the proper 4 of 4 and seemed to run to completion. For each subject: "[70/a6f467] NOTE: Process Eddy (ABCD_XXXX) terminated with an error exit status (2) -- Execution is retried (1)". The parallel structural processing seems to be proceeding fine thus far.

I have read that this could relate to RAM, but this error has persisted when devoting 64 gb of RAM to the task, and persisted when I attempted to run on multiple nodes. I have not changed any default settings of tractoflow, and the subjects do not have reverse encoded b0 files. Do you know what may cause this error? I can provide more info as needed.

Thanks,
Steven

^Minor¸Topup mean rev_b0 error when 3D data

There is a small issue with the command scil_image_math.py mean $rev_b0 $rev_b0 --data_type float32 -f in the topup process. If the rev_b0 is in 3D (which happens to be my case quite often), the scilpy script returns an error and tractoflow continues with the unchanged $rev_b0. This is only a minor issue, since all it implies is that the dtype of $rev_b0 remains unchanged (so probably int16 instead of float32). This is a small detail that only affects the Ants command right after, but I suggest to add a scil_image_math.py convert command to be sure that the processes are always with float32.

Adding Gibb's Ringing correction

Hi Guillaume Arnaud and JC,

Would it be possible to add a correction for Gibb's Ringing to the pipeline?

Thanks!

longitudinal option for T1 processes

Would it be possible to add an optional step after the N4 T1 process to create an unbiased intra-subject template ?

fmriprep is doing already this step with mri_robust_template from freesurfer.

I could work on this feature if you think tractoflow should have it.

Issues I could see :

• it adds a freesurfer dependency
• maybe a solution exists with ANTs but I'm not familiar with this software.

Final Tracking Files Appear to be Empty

Hello,

I ran Tractoflow on multiple subjects and the process completed with no errors according to the outfile produced by sbatch. I tried to import the .trk files into Trackvis, which said there were no fibers to be tracked. This was reaffirmed when I imported the .trk files into Vistasoft with 'read_trk_to_fg'.

I am confused by this output, since the images produced in the later processing stages all look correct. For example, I have attached below a screenshot from FSLView showing the V1 vector image modulated by the FA image (both in the results/DTI_Metrics folder). Do you know why this might be?

To provide a little more information, I am running Tractoflow on a Linux HPC system through the most recent Singularity container. The subjects did not have a reverse B0 image. The final tracking files are about 1 kb each. I'll be happy to provide more information or pictures as needed.

Thanks,
Steven

Features list

• Add workdir in output_dir
• Check version of nextflow
• Multi-shell Multi-tissue fODF [tractoflow 3.x]
• BIDS output [tractoflow 3.x]
• Think about QC

======
Old suggestions

• -Implement better registration step (https://www.biorxiv.org/content/10.1101/864108v2.full.pdf)
• -Add FSL bet for T1 (option)

Forgotten variable

The variable min_nvox in the nextflow.config does not appear in USAGE (nor in the read the doc).

Feature list for next releases

Done

• BIDS support
• Auto binding of external drive
• -Multiple seeds given for the tracking step
• -Support local Tracking algorithm
• -Gibbs correction

Feature list:

• -Add workdir in output_dir
• -Check version of nextflow
• -Add warning if some params are not good for replicability/reproducibility
• -Mutli-shell Multi-tissue fODF
• -Implement better registration step (https://www.biorxiv.org/content/10.1101/864108v2.full.pdf)
• -Add FSL bet for T1 (option)

Error while launching TractoFlow with singularity

Hello,

I have tried to launch TractoFlow on some "Penthera_3T" subject data downloaded from the address mentioned in the paper, and got the following error log file:

oct.-22 17:21:05.333 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /netapp/vol1_softs/TRACTOFLOW/2.0.1/main.nf --root /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T --dti_shells DTI_SHELLS --fodf_shells FODF_SHELLS --processes_brain_extraction_t1 1 --processes_registration 1 --output_dir /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T --processes 30 -with-singularity /netapp/vol1_softs/SINGULARITY/images/tractoflow/tractoflow_2.0.0_8b39aee_2019-04-26.img
oct.-22 17:21:05.466 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 19.04.0
oct.-22 17:21:05.486 [main] INFO  nextflow.cli.CmdRun - Launching `/netapp/vol1_softs/TRACTOFLOW/2.0.1/main.nf` [soggy_wescoff] - revision: 6d3eda526f
oct.-22 17:21:05.501 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /netapp/vol1_softs/TRACTOFLOW/2.0.1/nextflow.config
oct.-22 17:21:05.502 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /netapp/vol1_softs/TRACTOFLOW/2.0.1/nextflow.config
oct.-22 17:21:05.530 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
oct.-22 17:21:06.213 [main] DEBUG nextflow.config.ConfigBuilder - Enabling execution in Singularity container as requested by cli option `-with-singularity null`
oct.-22 17:21:06.238 [main] DEBUG nextflow.Session - Session uuid: f074cde9-3869-4130-96a8-4655dc30ac7d
oct.-22 17:21:06.238 [main] DEBUG nextflow.Session - Run name: soggy_wescoff
oct.-22 17:21:06.239 [main] DEBUG nextflow.Session - Executor pool size: 40
oct.-22 17:21:06.255 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 19.04.0 build 5069
  Modified: 17-04-2019 06:25 UTC (08:25 CEST)
  System: Linux 3.10.0-957.21.3.el7.x86_64
  Runtime: Groovy 2.5.6 on OpenJDK 64-Bit Server VM 1.8.0_222-b10
  Encoding: UTF-8 (UTF-8)
  Process: [email protected] [192.168.30.133]
  CPUs: 40 - Mem: 125.2 GB (119.6 GB) - Swap: 4 GB (3.2 GB)
oct.-22 17:21:06.295 [main] DEBUG nextflow.Session - Work-dir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work [nfs]
oct.-22 17:21:06.295 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /netapp/vol1_softs/TRACTOFLOW/2.0.1/bin
oct.-22 17:21:06.578 [main] DEBUG nextflow.Session - Session start invoked
oct.-22 17:21:06.582 [main] DEBUG nextflow.processor.TaskDispatcher - Dispatcher > start
oct.-22 17:21:06.585 [main] DEBUG nextflow.script.ScriptRunner - > Script parsing
oct.-22 17:21:07.201 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
oct.-22 17:21:07.209 [main] INFO  nextflow.Nextflow - TractoFlow pipeline
oct.-22 17:21:07.209 [main] INFO  nextflow.Nextflow - ===================
oct.-22 17:21:07.209 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.212 [main] INFO  nextflow.Nextflow - Start time: Tue Oct 22 17:21:06 CEST 2019
oct.-22 17:21:07.212 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.212 [main] DEBUG nextflow.Nextflow - [Command-line]
oct.-22 17:21:07.212 [main] DEBUG nextflow.Nextflow - nextflow run /netapp/vol1_softs/TRACTOFLOW/2.0.1/main.nf --root /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T --dti_shells DTI_SHELLS --fodf_shells FODF_SHELLS --processes_brain_extraction_t1 1 --processes_registration 1 --output_dir /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T --processes 30 -with-singularity /netapp/vol1_softs/SINGULARITY/images/tractoflow/tractoflow_2.0.0_8b39aee_2019-04-26.img
oct.-22 17:21:07.212 [main] DEBUG nextflow.Nextflow - 
oct.-22 17:21:07.212 [main] INFO  nextflow.Nextflow - [Git Info]
oct.-22 17:21:07.212 [main] INFO  nextflow.Nextflow - null - null [null]
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - Options
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - =======
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - [Denoise DWI]
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - Denoise DWI: true
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - [Topup]
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - Run Topup: true
oct.-22 17:21:07.213 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.214 [main] INFO  nextflow.Nextflow - [Eddy]
oct.-22 17:21:07.214 [main] INFO  nextflow.Nextflow - Run Eddy: true
oct.-22 17:21:07.214 [main] INFO  nextflow.Nextflow - Eddy command: eddy_openmp
oct.-22 17:21:07.214 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.214 [main] INFO  nextflow.Nextflow - [Resample DWI]
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - Resample DWI: true
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - Resolution: 1
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - [DTI shells]
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - DTI shells: DTI_SHELLS
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - [fODF shells]
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - fODF shells: FODF_SHELLS
oct.-22 17:21:07.215 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - [Compute fiber response function (FRF)]
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - Set FRF: false
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - FRF value: 15,4,4
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - [Mean FRF]
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - Mean FRF: true
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - [FODF Metrics]
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - FODF basis: descoteaux07
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - SH order: 8
oct.-22 17:21:07.216 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.217 [main] INFO  nextflow.Nextflow - [Seeding mask]
oct.-22 17:21:07.217 [main] INFO  nextflow.Nextflow - WM seeding: true
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - [PFT tracking]
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Algo: prob
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Seeding type: npv
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Number of seeds: 10
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Random seed: 0
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Step size: 0.1
oct.-22 17:21:07.218 [main] INFO  nextflow.Nextflow - Theta: 20
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Minimum length: 20
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Maximum length: 200
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - FODF basis: descoteaux07
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Compress streamlines: true
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Compressing threshold: 0.2
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Number of processes per tasks
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - =============================
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - T1 brain extraction: 1
oct.-22 17:21:07.219 [main] INFO  nextflow.Nextflow - Denoise DWI: 4
oct.-22 17:21:07.220 [main] INFO  nextflow.Nextflow - Denoise T1: 4
oct.-22 17:21:07.220 [main] INFO  nextflow.Nextflow - Eddy: 1
oct.-22 17:21:07.220 [main] INFO  nextflow.Nextflow - Compute fODF: 4
oct.-22 17:21:07.220 [main] INFO  nextflow.Nextflow - Registration: 1
oct.-22 17:21:07.220 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.221 [main] INFO  nextflow.Nextflow - Template T1 path
oct.-22 17:21:07.221 [main] INFO  nextflow.Nextflow - ================
oct.-22 17:21:07.221 [main] INFO  nextflow.Nextflow - Template T1: /human-data/mni_152_sym_09c/t1
oct.-22 17:21:07.221 [main] INFO  nextflow.Nextflow - 
oct.-22 17:21:07.222 [main] INFO  nextflow.Nextflow - Input: /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T
oct.-22 17:21:07.265 [PathVisitor-1] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T/; pattern: **/*{bval,bvec,dwi.nii.gz,t1.nii.gz}; options: [maxDepth:1]
oct.-22 17:21:07.347 [PathVisitor-2] DEBUG nextflow.file.PathVisitor - files for syntax: glob; folder: /netapp/vol2_agewell/pro/IMAP/imap_mvh/Penthera_3T/; pattern: **/*rev_b0.nii.gz; options: [maxDepth:1]
oct.-22 17:21:07.464 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.464 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.470 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.472 [main] INFO  nextflow.executor.Executor - [warm up] executor > local
oct.-22 17:21:07.477 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=30; memory=125.2 GB; capacity=40; pollInterval=100ms; dumpInterval=5m
oct.-22 17:21:07.481 [main] DEBUG nextflow.processor.TaskDispatcher - Starting monitor: LocalPollingMonitor
oct.-22 17:21:07.482 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
oct.-22 17:21:07.485 [main] DEBUG nextflow.executor.Executor - Invoke register for executor: local
oct.-22 17:21:07.515 [main] DEBUG nextflow.Session - >>> barrier register (process: README)
oct.-22 17:21:07.518 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > README -- maxForks: 40
oct.-22 17:21:07.552 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.552 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.552 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.554 [main] DEBUG nextflow.Session - >>> barrier register (process: Bet_Prelim_DWI)
oct.-22 17:21:07.554 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Bet_Prelim_DWI -- maxForks: 40
oct.-22 17:21:07.561 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.562 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.562 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.563 [main] DEBUG nextflow.Session - >>> barrier register (process: Denoise_DWI)
oct.-22 17:21:07.563 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Denoise_DWI -- maxForks: 40
oct.-22 17:21:07.581 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.581 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.581 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.583 [main] DEBUG nextflow.Session - >>> barrier register (process: Topup)
oct.-22 17:21:07.584 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Topup -- maxForks: 40
oct.-22 17:21:07.606 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.607 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.607 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.608 [main] DEBUG nextflow.Session - >>> barrier register (process: Eddy)
oct.-22 17:21:07.608 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Eddy -- maxForks: 40
oct.-22 17:21:07.625 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.626 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.626 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.627 [main] DEBUG nextflow.Session - >>> barrier register (process: Eddy_Topup)
oct.-22 17:21:07.628 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Eddy_Topup -- maxForks: 40
oct.-22 17:21:07.644 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.645 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.645 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.645 [main] DEBUG nextflow.Session - >>> barrier register (process: Extract_B0)
oct.-22 17:21:07.646 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Extract_B0 -- maxForks: 40
oct.-22 17:21:07.654 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.654 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.654 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.656 [main] DEBUG nextflow.Session - >>> barrier register (process: Bet_DWI)
oct.-22 17:21:07.657 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Bet_DWI -- maxForks: 40
oct.-22 17:21:07.664 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.665 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.665 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.666 [main] DEBUG nextflow.Session - >>> barrier register (process: N4_DWI)
oct.-22 17:21:07.666 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > N4_DWI -- maxForks: 40
oct.-22 17:21:07.670 [Actor Thread 1] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class java.util.Date -- Tue Oct 22 17:21:06 CEST 2019
oct.-22 17:21:07.674 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.674 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.674 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.675 [main] DEBUG nextflow.Session - >>> barrier register (process: Crop_DWI)
oct.-22 17:21:07.675 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Crop_DWI -- maxForks: 40
oct.-22 17:21:07.683 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.683 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.683 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.684 [main] DEBUG nextflow.Session - >>> barrier register (process: Denoise_T1)
oct.-22 17:21:07.684 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Denoise_T1 -- maxForks: 40
oct.-22 17:21:07.688 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.688 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.688 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.688 [main] DEBUG nextflow.Session - >>> barrier register (process: N4_T1)
oct.-22 17:21:07.689 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > N4_T1 -- maxForks: 40
oct.-22 17:21:07.693 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.693 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.693 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.693 [main] DEBUG nextflow.Session - >>> barrier register (process: Resample_T1)
oct.-22 17:21:07.694 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Resample_T1 -- maxForks: 40
oct.-22 17:21:07.697 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.697 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.697 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.698 [main] DEBUG nextflow.Session - >>> barrier register (process: Bet_T1)
oct.-22 17:21:07.698 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Bet_T1 -- maxForks: 40
oct.-22 17:21:07.701 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.701 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.701 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.702 [main] DEBUG nextflow.Session - >>> barrier register (process: Crop_T1)
oct.-22 17:21:07.702 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Crop_T1 -- maxForks: 40
oct.-22 17:21:07.709 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.709 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.710 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.712 [main] DEBUG nextflow.Session - >>> barrier register (process: Normalize_DWI)
oct.-22 17:21:07.713 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Normalize_DWI -- maxForks: 40
oct.-22 17:21:07.719 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.719 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.720 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.720 [main] DEBUG nextflow.Session - >>> barrier register (process: Resample_DWI)
oct.-22 17:21:07.720 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Resample_DWI -- maxForks: 40
oct.-22 17:21:07.725 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.725 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.725 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.725 [main] DEBUG nextflow.Session - >>> barrier register (process: Resample_B0)
oct.-22 17:21:07.726 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Resample_B0 -- maxForks: 40
oct.-22 17:21:07.730 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.730 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.730 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.730 [main] DEBUG nextflow.Session - >>> barrier register (process: Extract_DTI_Shell)
oct.-22 17:21:07.730 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Extract_DTI_Shell -- maxForks: 40
oct.-22 17:21:07.741 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.741 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.742 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.742 [main] DEBUG nextflow.Session - >>> barrier register (process: DTI_Metrics)
oct.-22 17:21:07.742 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > DTI_Metrics -- maxForks: 40
oct.-22 17:21:07.746 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.746 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.747 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.747 [main] DEBUG nextflow.Session - >>> barrier register (process: Extract_FODF_Shell)
oct.-22 17:21:07.747 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Extract_FODF_Shell -- maxForks: 40
oct.-22 17:21:07.754 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.754 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.754 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.754 [main] DEBUG nextflow.Session - >>> barrier register (process: Register_T1)
oct.-22 17:21:07.755 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Register_T1 -- maxForks: 40
oct.-22 17:21:07.758 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.758 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.758 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.759 [main] DEBUG nextflow.Session - >>> barrier register (process: Segment_Tissues)
oct.-22 17:21:07.759 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Segment_Tissues -- maxForks: 40
oct.-22 17:21:07.763 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.763 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.764 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.764 [main] DEBUG nextflow.Session - >>> barrier register (process: Compute_FRF)
oct.-22 17:21:07.764 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Compute_FRF -- maxForks: 40
oct.-22 17:21:07.774 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.774 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.774 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.775 [main] DEBUG nextflow.Session - >>> barrier register (process: Mean_FRF)
oct.-22 17:21:07.775 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Mean_FRF -- maxForks: 40
oct.-22 17:21:07.786 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.787 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.787 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.787 [main] DEBUG nextflow.Session - >>> barrier register (process: FODF_Metrics)
oct.-22 17:21:07.787 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.787 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > FODF_Metrics -- maxForks: 40
oct.-22 17:21:07.791 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.791 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.791 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.791 [main] DEBUG nextflow.Session - >>> barrier register (process: PFT_Maps)
oct.-22 17:21:07.791 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > PFT_Maps -- maxForks: 40
oct.-22 17:21:07.794 [Task submitter] INFO  nextflow.Session - [36/43dadc] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:07.795 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.795 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.795 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.795 [main] DEBUG nextflow.Session - >>> barrier register (process: Seeding_Mask)
oct.-22 17:21:07.795 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Seeding_Mask -- maxForks: 40
oct.-22 17:21:07.799 [main] DEBUG nextflow.processor.ProcessFactory - << taskConfig executor: null
oct.-22 17:21:07.800 [main] DEBUG nextflow.processor.ProcessFactory - >> processorType: 'local'
oct.-22 17:21:07.800 [main] DEBUG nextflow.executor.Executor - Initializing executor: local
oct.-22 17:21:07.800 [main] DEBUG nextflow.Session - >>> barrier register (process: Tracking)
oct.-22 17:21:07.802 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Tracking -- maxForks: 40
oct.-22 17:21:07.802 [main] DEBUG nextflow.script.ScriptRunner - > Await termination 
oct.-22 17:21:07.802 [main] DEBUG nextflow.Session - Session await
oct.-22 17:21:07.813 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.814 [Task submitter] INFO  nextflow.Session - [8f/944868] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:07.854 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.855 [Task submitter] INFO  nextflow.Session - [cb/1a086f] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:07.880 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.881 [Task submitter] INFO  nextflow.Session - [1f/eef9c6] Submitted process > Denoise_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:07.915 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.915 [Task submitter] INFO  nextflow.Session - [57/25f4ea] Submitted process > Denoise_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:07.957 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.958 [Task submitter] INFO  nextflow.Session - [ee/b1090c] Submitted process > Denoise_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:07.998 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:07.999 [Task submitter] INFO  nextflow.Session - [16/df8728] Submitted process > Denoise_T1 (sub-PT001_ses-2_acq-1)
oct.-22 17:21:08.047 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:08.048 [Task submitter] INFO  nextflow.Session - [fb/ec8803] Submitted process > Denoise_T1 (sub-PT001_ses-1_acq-2)
oct.-22 17:21:08.069 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:08.070 [Task submitter] INFO  nextflow.Session - [a6/ad1fe7] Submitted process > README (README)
oct.-22 17:21:08.089 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:08.090 [Task submitter] INFO  nextflow.Session - [ce/aa5014] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:09.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: README (README); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a6/ad1fe7dbc7e3a71a6aa2d7c431563e]
oct.-22 17:21:09.679 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a6/ad1fe7] NOTE: Process `README (README)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:09.680 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:09.683 [Task submitter] INFO  nextflow.Session - [9a/d88eab] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:10.061 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: Denoise_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/57/25f4ea6c9b95f3402526b4bd988f7d]
oct.-22 17:21:10.064 [Task monitor] INFO  nextflow.processor.TaskProcessor - [57/25f4ea] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.092 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.092 [Task submitter] INFO  nextflow.Session - [19/bf2ac1] Submitted process > Denoise_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:10.256 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 24; name: Denoise_T1 (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/16/df87286c4d96c644d51710d119f856]
oct.-22 17:21:10.258 [Task monitor] INFO  nextflow.processor.TaskProcessor - [16/df8728] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.281 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 22; name: Denoise_T1 (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/fb/ec8803f718ac85d9410b77b8fac3eb]
oct.-22 17:21:10.282 [Task monitor] INFO  nextflow.processor.TaskProcessor - [fb/ec8803] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.288 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.288 [Task submitter] INFO  nextflow.Session - [99/9fe3ef] Submitted process > Denoise_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:10.315 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.316 [Task submitter] INFO  nextflow.Session - [83/2175fc] Submitted process > Denoise_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:10.660 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/36/43dadca5e44462636351b086ff8c8e]
oct.-22 17:21:10.662 [Task monitor] INFO  nextflow.processor.TaskProcessor - [36/43dadc] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.684 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.684 [Task submitter] INFO  nextflow.Session - [2b/a2f695] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:10.694 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: Denoise_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/1f/eef9c6d5d30fd0d67777ea5b3292c5]
oct.-22 17:21:10.695 [Task monitor] INFO  nextflow.processor.TaskProcessor - [1f/eef9c6] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.709 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8f/94486876d89382a7fb95f89ede390a]
oct.-22 17:21:10.710 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8f/944868] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.741 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.742 [Task submitter] INFO  nextflow.Session - [92/491556] Submitted process > Denoise_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:10.776 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.776 [Task submitter] INFO  nextflow.Session - [98/8043a9] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:10.791 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: Denoise_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/ee/b1090cf2fb6e9d7f07be457e5481b6]
oct.-22 17:21:10.792 [Task monitor] INFO  nextflow.processor.TaskProcessor - [ee/b1090c] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.801 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/cb/1a086fc09276cd9bf867e2e683fcb0]
oct.-22 17:21:10.802 [Task monitor] INFO  nextflow.processor.TaskProcessor - [cb/1a086f] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/ce/aa501434c041d807e6e37c13fa514c]
oct.-22 17:21:10.804 [Task monitor] INFO  nextflow.processor.TaskProcessor - [ce/aa5014] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:10.825 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.826 [Task submitter] INFO  nextflow.Session - [0c/1ce29f] Submitted process > Denoise_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:10.852 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:10.852 [Task submitter] INFO  nextflow.Session - [c7/eb2d56] Submitted process > Denoise_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:11.246 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/9a/d88eab31907e8b94e0d951347e97ee]
oct.-22 17:21:11.247 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9a/d88eab] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:11.272 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:11.273 [Task submitter] INFO  nextflow.Session - [b4/1e12f8] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:11.699 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: Denoise_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/19/bf2ac1842445338509111853ff179b]
oct.-22 17:21:11.701 [Task monitor] INFO  nextflow.processor.TaskProcessor - [19/bf2ac1] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:11.735 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:11.735 [Task submitter] INFO  nextflow.Session - [9c/2eb308] Submitted process > Denoise_T1 (sub-PT001_ses-1_acq-1)
oct.-22 17:21:11.922 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: Denoise_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/83/2175fc5148539c72c243a49a7c0540]
oct.-22 17:21:11.924 [Task monitor] INFO  nextflow.processor.TaskProcessor - [83/2175fc] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:11.961 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:11.962 [Task submitter] INFO  nextflow.Session - [77/bedc84] Submitted process > Denoise_T1 (sub-PT001_ses-3_acq-1)
oct.-22 17:21:12.100 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: Denoise_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/99/9fe3ef696516520332af1840b315e3]
oct.-22 17:21:12.102 [Task monitor] INFO  nextflow.processor.TaskProcessor - [99/9fe3ef] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.139 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.140 [Task submitter] INFO  nextflow.Session - [0a/18254b] Submitted process > Denoise_T1 (sub-PT001_ses-3_acq-2)
oct.-22 17:21:12.435 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 18; name: Denoise_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/0c/1ce29f4476cac7c861780d1fc47aad]
oct.-22 17:21:12.437 [Task monitor] INFO  nextflow.processor.TaskProcessor - [0c/1ce29f] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.443 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.444 [Task submitter] INFO  nextflow.Session - [f5/72c751] Submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:12.518 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.518 [Task submitter] INFO  nextflow.Session - [9e/c0b9e4] Re-submitted process > README (README)
oct.-22 17:21:12.630 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: Denoise_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/c7/eb2d561360af7776c9f1526e8cfa96]
oct.-22 17:21:12.635 [Task monitor] INFO  nextflow.processor.TaskProcessor - [c7/eb2d56] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.644 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.644 [Task submitter] INFO  nextflow.Session - [69/fca2fc] Submitted process > Denoise_T1 (sub-PT001_ses-2_acq-3)
oct.-22 17:21:12.746 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/2b/a2f695985bdcc1b62fd42299779a14]
oct.-22 17:21:12.747 [Task monitor] INFO  nextflow.processor.TaskProcessor - [2b/a2f695] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.751 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 19; name: Denoise_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/92/491556888418364b1b2e1c39a46608]
oct.-22 17:21:12.752 [Task monitor] INFO  nextflow.processor.TaskProcessor - [92/491556] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.753 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.754 [Task submitter] INFO  nextflow.Session - [1a/11fac8] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:12.755 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/98/8043a90063733464d2276586600860]
oct.-22 17:21:12.756 [Task monitor] INFO  nextflow.processor.TaskProcessor - [98/8043a9] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.789 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.789 [Task submitter] INFO  nextflow.Session - [f2/68a458] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:12.825 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.826 [Task submitter] INFO  nextflow.Session - [a9/8c457b] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:12.845 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/b4/1e12f803115a91d9eadf193b9807da]
oct.-22 17:21:12.846 [Task monitor] INFO  nextflow.processor.TaskProcessor - [b4/1e12f8] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:12.866 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:12.866 [Task submitter] INFO  nextflow.Session - [fa/a5bcc2] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:13.369 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 21; name: Denoise_T1 (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/9c/2eb308c5820c5138fefc5356796755]
oct.-22 17:21:13.371 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9c/2eb308] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:13.417 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:13.417 [Task submitter] INFO  nextflow.Session - [e1/46e8c9] Submitted process > Denoise_T1 (sub-PT001_ses-2_acq-2)
oct.-22 17:21:13.532 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 23; name: Denoise_T1 (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/77/bedc8425767c6b493bd735c8ec5272]
oct.-22 17:21:13.533 [Task monitor] INFO  nextflow.processor.TaskProcessor - [77/bedc84] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:13.562 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:13.563 [Task submitter] INFO  nextflow.Session - [82/3c8e32] Submitted process > Denoise_T1 (sub-PT001_ses-3_acq-3)
oct.-22 17:21:13.747 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 25; name: Denoise_T1 (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/0a/18254b656b8131afbd820a2597d1de]
oct.-22 17:21:13.748 [Task monitor] INFO  nextflow.processor.TaskProcessor - [0a/18254b] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:13.755 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:13.756 [Task submitter] INFO  nextflow.Session - [f4/ebad5c] Submitted process > Denoise_T1 (sub-PT001_ses-1_acq-3)
oct.-22 17:21:14.070 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 29; name: README (README); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/9e/c0b9e4001d4e5e2bb27f0bb87b9e4e]
oct.-22 17:21:14.070 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9e/c0b9e4] NOTE: Process `README (README)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:14.079 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f5/72c7514c3a46403a824d98243351bf]
oct.-22 17:21:14.080 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f5/72c751] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:14.095 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.095 [Task submitter] INFO  nextflow.Session - [3b/928c77] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:14.106 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.107 [Task submitter] INFO  nextflow.Session - [0a/4b9718] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:14.215 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 20; name: Denoise_T1 (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/69/fca2fc92360fbba8e541eb727a19c0]
oct.-22 17:21:14.216 [Task monitor] INFO  nextflow.processor.TaskProcessor - [69/fca2fc] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:14.234 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.235 [Task submitter] INFO  nextflow.Session - [28/7652b1] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:14.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 34; name: Denoise_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f2/68a4589446d5799d22ceac5d6fb6ac]
oct.-22 17:21:14.357 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f2/68a458] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:14.369 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.370 [Task submitter] INFO  nextflow.Session - [d7/6df60e] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-1)
oct.-22 17:21:14.387 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 37; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/fa/a5bcc2299abae60808c30e4e9a4d96]
oct.-22 17:21:14.389 [Task monitor] INFO  nextflow.processor.TaskProcessor - [fa/a5bcc2] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:14.398 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 33; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/1a/11fac8dc34b9d05178af4f0188309f]
oct.-22 17:21:14.398 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.398 [Task submitter] INFO  nextflow.Session - [04/b8ef00] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:14.399 [Task monitor] INFO  nextflow.processor.TaskProcessor - [1a/11fac8] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:14.402 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 35; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a9/8c457b625bf04d11bec8ee61acaea7]
oct.-22 17:21:14.403 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a9/8c457b] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:14.459 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.460 [Task submitter] INFO  nextflow.Session - [15/29ea40] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:14.470 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:14.471 [Task submitter] INFO  nextflow.Session - [cc/779fb8] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:15.040 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 27; name: Denoise_T1 (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/e1/46e8c9ef93568f9a84e1f2b400fff9]
oct.-22 17:21:15.041 [Task monitor] INFO  nextflow.processor.TaskProcessor - [e1/46e8c9] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:15.079 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.079 [Task submitter] INFO  nextflow.Session - [6e/b24baf] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-2)
oct.-22 17:21:15.183 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 28; name: Denoise_T1 (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/82/3c8e32209bdaa26edb56c947b5eb2b]
oct.-22 17:21:15.185 [Task monitor] INFO  nextflow.processor.TaskProcessor - [82/3c8e32] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:15.228 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.228 [Task submitter] INFO  nextflow.Session - [25/fa3e76] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:15.356 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 26; name: Denoise_T1 (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f4/ebad5c356d1daf7fda213294930368]
oct.-22 17:21:15.358 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f4/ebad5c] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (1)
oct.-22 17:21:15.390 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.390 [Task submitter] INFO  nextflow.Session - [f0/390bdd] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:15.674 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 38; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/3b/928c77e497a45ad2eaeb7d833b2d8c]
oct.-22 17:21:15.676 [Task monitor] INFO  nextflow.processor.TaskProcessor - [3b/928c77] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:15.680 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 39; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/0a/4b9718e41afd5c0bbf3d028bf628d7]
oct.-22 17:21:15.681 [Task monitor] INFO  nextflow.processor.TaskProcessor - [0a/4b9718] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:15.710 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.710 [Task submitter] INFO  nextflow.Session - [7c/079bcb] Re-submitted process > README (README)
oct.-22 17:21:15.741 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.741 [Task submitter] INFO  nextflow.Session - [c5/8f17a5] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:15.818 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 30; name: Denoise_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/28/7652b14ebba826f97365f4a9a407ab]
oct.-22 17:21:15.820 [Task monitor] INFO  nextflow.processor.TaskProcessor - [28/7652b1] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:15.836 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.836 [Task submitter] INFO  nextflow.Session - [f2/13fac0] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:15.876 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 31; name: Denoise_T1 (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/d7/6df60e1b8042ebcd53e411630a695d]
oct.-22 17:21:15.877 [Task monitor] INFO  nextflow.processor.TaskProcessor - [d7/6df60e] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:15.894 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.895 [Task submitter] INFO  nextflow.Session - [e2/8c5eaf] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:15.964 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 45; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/04/b8ef00d335d540429c4a6ea4798a5b]
oct.-22 17:21:15.965 [Task monitor] INFO  nextflow.processor.TaskProcessor - [04/b8ef00] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:15.972 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:15.972 [Task submitter] INFO  nextflow.Session - [9e/a9f1f6] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:16.042 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 47; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/15/29ea406d43a9ea1460a2334fbbac3b]
oct.-22 17:21:16.043 [Task monitor] INFO  nextflow.processor.TaskProcessor - [15/29ea40] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:16.046 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 48; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/cc/779fb8af4b95d1212cbfef8dc553fb]
oct.-22 17:21:16.047 [Task monitor] INFO  nextflow.processor.TaskProcessor - [cc/779fb8] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:16.049 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:16.049 [Task submitter] INFO  nextflow.Session - [ca/9c4031] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:16.056 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:16.056 [Task submitter] INFO  nextflow.Session - [98/51a23a] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:16.651 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 32; name: Denoise_T1 (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/6e/b24baf57ed068bcff9bb170dc5b2c4]
oct.-22 17:21:16.652 [Task monitor] INFO  nextflow.processor.TaskProcessor - [6e/b24baf] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:16.660 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:16.661 [Task submitter] INFO  nextflow.Session - [99/108d59] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:16.822 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 36; name: Denoise_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/25/fa3e762b46a2af6680fbf4a393819c]
oct.-22 17:21:16.824 [Task monitor] INFO  nextflow.processor.TaskProcessor - [25/fa3e76] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:16.848 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:16.848 [Task submitter] INFO  nextflow.Session - [5b/934f81] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:16.995 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 40; name: Denoise_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f0/390bdda46ede45f5e5b4a5a9ece943]
oct.-22 17:21:16.996 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f0/390bdd] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:17.034 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.035 [Task submitter] INFO  nextflow.Session - [c2/100d1b] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:17.239 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 52; name: README (README); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/7c/079bcb2bbfd009605fa86678efccf4]
oct.-22 17:21:17.240 [Task monitor] INFO  nextflow.processor.TaskProcessor - [7c/079bcb] NOTE: Process `README (README)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:17.258 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.258 [Task submitter] INFO  nextflow.Session - [a0/390a13] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:17.315 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 53; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/c5/8f17a51699fc02ef82552f2acc00f2]
oct.-22 17:21:17.317 [Task monitor] INFO  nextflow.processor.TaskProcessor - [c5/8f17a5] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:17.347 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.348 [Task submitter] INFO  nextflow.Session - [ab/0001b6] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:17.395 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 41; name: Denoise_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f2/13fac0d03f1ac8b76b35dc7ba960eb]
oct.-22 17:21:17.396 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f2/13fac0] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:17.414 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.414 [Task submitter] INFO  nextflow.Session - [06/8ac31c] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-1)
oct.-22 17:21:17.450 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 42; name: Denoise_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/e2/8c5eafd2b2633c0ccaa7f695213383]
oct.-22 17:21:17.451 [Task monitor] INFO  nextflow.processor.TaskProcessor - [e2/8c5eaf] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:17.479 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.479 [Task submitter] INFO  nextflow.Session - [90/e13fb3] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-1)
oct.-22 17:21:17.538 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 56; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/9e/a9f1f6e9b6f69d0e637191896b4d34]
oct.-22 17:21:17.539 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9e/a9f1f6] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:17.559 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.559 [Task submitter] INFO  nextflow.Session - [93/1f5f24] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:17.592 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 58; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/ca/9c4031b6823545faf3e4b9dbc3a4c0]
oct.-22 17:21:17.593 [Task monitor] INFO  nextflow.processor.TaskProcessor - [ca/9c4031] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:17.611 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.611 [Task submitter] INFO  nextflow.Session - [10/a9e14a] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:17.621 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 57; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/98/51a23ab4dca8dabd6015a72158155d]
oct.-22 17:21:17.623 [Task monitor] INFO  nextflow.processor.TaskProcessor - [98/51a23a] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:17.639 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:17.640 [Task submitter] INFO  nextflow.Session - [1b/9f1dba] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:18.257 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 43; name: Denoise_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/99/108d59a308baad28018f7ee02ef5b1]
oct.-22 17:21:18.258 [Task monitor] INFO  nextflow.processor.TaskProcessor - [99/108d59] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:18.281 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.281 [Task submitter] INFO  nextflow.Session - [4a/5b9025] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-2)
oct.-22 17:21:18.453 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 44; name: Denoise_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/5b/934f8156b7bc9e4d9395521eb2ba3f]
oct.-22 17:21:18.455 [Task monitor] INFO  nextflow.processor.TaskProcessor - [5b/934f81] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:18.479 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.479 [Task submitter] INFO  nextflow.Session - [22/2a24cc] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-3)
oct.-22 17:21:18.610 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 46; name: Denoise_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/c2/100d1b0d492bbdb951f95b45c7722e]
oct.-22 17:21:18.611 [Task monitor] INFO  nextflow.processor.TaskProcessor - [c2/100d1b] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:18.630 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.630 [Task submitter] INFO  nextflow.Session - [35/79ab1c] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:18.828 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 62; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a0/390a1359fc3fde293fdcce7d244e8c]
oct.-22 17:21:18.829 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a0/390a13] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:18.847 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.847 [Task submitter] INFO  nextflow.Session - [a8/441cca] Re-submitted process > README (README)
oct.-22 17:21:18.942 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 63; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/ab/0001b6ec4bac25d33ccc545e74f3b3]
oct.-22 17:21:18.943 [Task monitor] INFO  nextflow.processor.TaskProcessor - [ab/0001b6] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:18.944 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 49; name: Denoise_T1 (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/06/8ac31cccc6dd81d24d9d20904a4f5e]
oct.-22 17:21:18.945 [Task monitor] INFO  nextflow.processor.TaskProcessor - [06/8ac31c] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:18.972 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.972 [Task submitter] INFO  nextflow.Session - [8b/d2f7ef] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:18.998 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:18.999 [Task submitter] INFO  nextflow.Session - [9f/cced74] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:19.000 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 50; name: Denoise_T1 (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/90/e13fb38b6fd71d1c3de4dea054ffa6]
oct.-22 17:21:19.002 [Task monitor] INFO  nextflow.processor.TaskProcessor - [90/e13fb3] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:19.034 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:19.034 [Task submitter] INFO  nextflow.Session - [88/1ad794] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-2)
oct.-22 17:21:19.127 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 66; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/93/1f5f2457b512891e114826d3d3c3ca]
oct.-22 17:21:19.128 [Task monitor] INFO  nextflow.processor.TaskProcessor - [93/1f5f24] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:19.132 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 67; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/10/a9e14aeec42b11bfbd63ab52e37b0e]
oct.-22 17:21:19.132 [Task monitor] INFO  nextflow.processor.TaskProcessor - [10/a9e14a] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:19.157 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:19.158 [Task submitter] INFO  nextflow.Session - [75/2bcc6d] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:19.181 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 68; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/1b/9f1dba7a6650b0aa90373f66efbe7b]
oct.-22 17:21:19.182 [Task monitor] INFO  nextflow.processor.TaskProcessor - [1b/9f1dba] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:19.195 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:19.195 [Task submitter] INFO  nextflow.Session - [a7/ba52e2] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:19.223 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:19.224 [Task submitter] INFO  nextflow.Session - [1e/930a99] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:19.816 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 51; name: Denoise_T1 (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/4a/5b9025b3360685f516756135483324]
oct.-22 17:21:19.818 [Task monitor] INFO  nextflow.processor.TaskProcessor - [4a/5b9025] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:19.825 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:19.825 [Task submitter] INFO  nextflow.Session - [e0/fdaec9] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-3)
oct.-22 17:21:20.033 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 54; name: Denoise_T1 (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/22/2a24cc355ffa28bbcba55a6a989f4f]
oct.-22 17:21:20.034 [Task monitor] INFO  nextflow.processor.TaskProcessor - [22/2a24cc] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:20.061 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.061 [Task submitter] INFO  nextflow.Session - [38/e96a8f] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-3)
oct.-22 17:21:20.206 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 55; name: Denoise_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/35/79ab1c2f04e0107db8b21813f7c3ae]
oct.-22 17:21:20.208 [Task monitor] INFO  nextflow.processor.TaskProcessor - [35/79ab1c] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:20.232 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.233 [Task submitter] INFO  nextflow.Session - [20/2d0479] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:20.400 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 72; name: README (README); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a8/441cca0007967d8cf40c094ee7f11f]
oct.-22 17:21:20.401 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a8/441cca] NOTE: Process `README (README)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:20.405 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: README)
oct.-22 17:21:20.424 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.424 [Task submitter] INFO  nextflow.Session - [8c/c06434] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:20.514 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 73; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8b/d2f7efb77db57cc72d6fc66f96ebc4]
oct.-22 17:21:20.515 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8b/d2f7ef] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:20.534 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 74; name: Denoise_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/9f/cced746a17c0e6b248fbe7c587bebd]
oct.-22 17:21:20.534 [Task monitor] INFO  nextflow.processor.TaskProcessor - [9f/cced74] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:20.550 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 59; name: Denoise_T1 (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/88/1ad794ac89e86f629a08ecbc66e95e]
oct.-22 17:21:20.551 [Task monitor] INFO  nextflow.processor.TaskProcessor - [88/1ad794] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:20.555 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.556 [Task submitter] INFO  nextflow.Session - [17/d6dd31] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:20.566 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.566 [Task submitter] INFO  nextflow.Session - [99/e582ad] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-1)
oct.-22 17:21:20.599 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.599 [Task submitter] INFO  nextflow.Session - [89/9cd904] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-1)
oct.-22 17:21:20.702 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 76; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/75/2bcc6d2fcfcc391dc2d129725334ef]
oct.-22 17:21:20.703 [Task monitor] INFO  nextflow.processor.TaskProcessor - [75/2bcc6d] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:20.732 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.732 [Task submitter] INFO  nextflow.Session - [8d/4baf8b] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:20.743 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 77; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a7/ba52e26559106c67ed539827636456]
oct.-22 17:21:20.743 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a7/ba52e2] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:20.773 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.773 [Task submitter] INFO  nextflow.Session - [c0/0c68a8] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:20.777 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 78; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/1e/930a99dacc0bbdc83bc385f634c7ce]
oct.-22 17:21:20.778 [Task monitor] INFO  nextflow.processor.TaskProcessor - [1e/930a99] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:20.809 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:20.809 [Task submitter] INFO  nextflow.Session - [8a/19a13d] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:21.370 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 60; name: Denoise_T1 (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/e0/fdaec954d6d8a73b3fbb668b028f9f]
oct.-22 17:21:21.371 [Task monitor] INFO  nextflow.processor.TaskProcessor - [e0/fdaec9] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:21.391 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:21.391 [Task submitter] INFO  nextflow.Session - [f1/0dafbe] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-1)
oct.-22 17:21:21.634 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 61; name: Denoise_T1 (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/38/e96a8fc86999a3689244ec18bf5679]
oct.-22 17:21:21.635 [Task monitor] INFO  nextflow.processor.TaskProcessor - [38/e96a8f] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (2)
oct.-22 17:21:21.642 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:21.642 [Task submitter] INFO  nextflow.Session - [18/29b0b7] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-2)
oct.-22 17:21:21.763 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 64; name: Denoise_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/20/2d04793e0b6c5fb1aa1fa22b859943]
oct.-22 17:21:21.764 [Task monitor] INFO  nextflow.processor.TaskProcessor - [20/2d0479] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:21.797 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:21.798 [Task submitter] INFO  nextflow.Session - [be/ab761c] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:22.060 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 82; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8c/c06434484d4ed488fe7dafb09f8f18]
oct.-22 17:21:22.061 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8c/c06434] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:22.066 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.066 [Task submitter] INFO  nextflow.Session - [aa/97b128] Re-submitted process > Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:22.098 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 84; name: Denoise_T1 (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/99/e582ad67d84647d0075cc90081ce7a]
oct.-22 17:21:22.100 [Task monitor] INFO  nextflow.processor.TaskProcessor - [99/e582ad] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:22.103 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 85; name: Denoise_T1 (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/89/9cd904bcbafad2b880411a5f45b8cd]
oct.-22 17:21:22.104 [Task monitor] INFO  nextflow.processor.TaskProcessor - [89/9cd904] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:22.104 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.105 [Task submitter] INFO  nextflow.Session - [78/5d3612] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:22.114 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 83; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/17/d6dd311bd830e4ffc88ce7f2961706]
oct.-22 17:21:22.115 [Task monitor] INFO  nextflow.processor.TaskProcessor - [17/d6dd31] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:22.129 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.129 [Task submitter] INFO  nextflow.Session - [29/ff1e51] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:22.326 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 86; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8d/4baf8ba7f81e6b54062b424b2a0ea8]
oct.-22 17:21:22.327 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8d/4baf8b] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:22.339 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 87; name: Bet_Prelim_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/c0/0c68a81563d2bd506688aa0644d840]
oct.-22 17:21:22.340 [Task monitor] INFO  nextflow.processor.TaskProcessor - [c0/0c68a8] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:22.349 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.349 [Task submitter] INFO  nextflow.Session - [66/0acfda] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:22.350 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 88; name: Bet_Prelim_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8a/19a13d8b3b4e6ee00a16a603bc53b2]
oct.-22 17:21:22.351 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8a/19a13d] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:22.389 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.390 [Task submitter] INFO  nextflow.Session - [6b/688387] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:22.949 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 65; name: Denoise_T1 (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f1/0dafbef4179beae2a4545eb64723b1]
oct.-22 17:21:22.953 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f1/0dafbe] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:22.986 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:22.987 [Task submitter] INFO  nextflow.Session - [fd/84fc15] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:23.166 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 69; name: Denoise_T1 (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/18/29b0b7caae89838fef8dc608125acc]
oct.-22 17:21:23.167 [Task monitor] INFO  nextflow.processor.TaskProcessor - [18/29b0b7] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.173 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.173 [Task submitter] INFO  nextflow.Session - [b3/15a505] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-2)
oct.-22 17:21:23.408 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 70; name: Denoise_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/be/ab761cb7f51a34eaabf2fa81fb3838]
oct.-22 17:21:23.409 [Task monitor] INFO  nextflow.processor.TaskProcessor - [be/ab761c] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.436 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.436 [Task submitter] INFO  nextflow.Session - [a1/a964c6] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-3)
oct.-22 17:21:23.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 92; name: Bet_Prelim_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/aa/97b128d83c885d90c6c29ff552f879]
oct.-22 17:21:23.648 [Task monitor] INFO  nextflow.processor.TaskProcessor - [aa/97b128] NOTE: Process `Bet_Prelim_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:23.650 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Bet_Prelim_DWI)
oct.-22 17:21:23.672 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 71; name: Denoise_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/78/5d36121d2653756359338b9d315d2e]
oct.-22 17:21:23.673 [Task monitor] INFO  nextflow.processor.TaskProcessor - [78/5d3612] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.678 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 75; name: Denoise_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/29/ff1e51200097fb3c140c81e4a3216a]
oct.-22 17:21:23.679 [Task monitor] INFO  nextflow.processor.TaskProcessor - [29/ff1e51] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.723 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.723 [Task submitter] INFO  nextflow.Session - [5f/db2fb6] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-1)
oct.-22 17:21:23.731 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.731 [Task submitter] INFO  nextflow.Session - [0a/eb0c0a] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-1)
oct.-22 17:21:23.918 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 79; name: Denoise_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/66/0acfda0422f55c598a3540ecc939ea]
oct.-22 17:21:23.919 [Task monitor] INFO  nextflow.processor.TaskProcessor - [66/0acfda] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.935 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.936 [Task submitter] INFO  nextflow.Session - [4d/1e88ed] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-2)
oct.-22 17:21:23.947 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 80; name: Denoise_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/6b/68838729366a4eb2549b09b9b210d4]
oct.-22 17:21:23.948 [Task monitor] INFO  nextflow.processor.TaskProcessor - [6b/688387] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:23.955 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:23.955 [Task submitter] INFO  nextflow.Session - [06/f21f51] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-3)
oct.-22 17:21:24.569 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 81; name: Denoise_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/fd/84fc15e84f9dc6471c5ffad7e17156]
oct.-22 17:21:24.570 [Task monitor] INFO  nextflow.processor.TaskProcessor - [fd/84fc15] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:24.577 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:24.577 [Task submitter] INFO  nextflow.Session - [f1/8d1737] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-3)
oct.-22 17:21:24.724 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 89; name: Denoise_T1 (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/b3/15a505b3d025d980dbe0b8a48349cc]
oct.-22 17:21:24.726 [Task monitor] INFO  nextflow.processor.TaskProcessor - [b3/15a505] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:24.763 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:24.764 [Task submitter] INFO  nextflow.Session - [e8/38850a] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-1)
oct.-22 17:21:24.946 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 90; name: Denoise_T1 (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/a1/a964c6cfc3e7d8eb5fe7c5c70d8159]
oct.-22 17:21:24.947 [Task monitor] INFO  nextflow.processor.TaskProcessor - [a1/a964c6] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:24.975 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:24.975 [Task submitter] INFO  nextflow.Session - [d1/21ee24] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-1)
oct.-22 17:21:25.273 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 93; name: Denoise_DWI (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/0a/eb0c0aec726db4547c5121fea14e85]
oct.-22 17:21:25.274 [Task monitor] INFO  nextflow.processor.TaskProcessor - [0a/eb0c0a] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:25.282 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:25.282 [Task submitter] INFO  nextflow.Session - [8f/0e7967] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-1)
oct.-22 17:21:25.287 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 91; name: Denoise_DWI (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/5f/db2fb629fe3fb55128f9248c8c4a37]
oct.-22 17:21:25.288 [Task monitor] INFO  nextflow.processor.TaskProcessor - [5f/db2fb6] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:25.313 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:25.314 [Task submitter] INFO  nextflow.Session - [95/f450f8] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-1)
oct.-22 17:21:25.457 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 94; name: Denoise_T1 (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/4d/1e88edd2b9a520b020eb6ba2c934a2]
oct.-22 17:21:25.459 [Task monitor] INFO  nextflow.processor.TaskProcessor - [4d/1e88ed] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:25.466 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:25.466 [Task submitter] INFO  nextflow.Session - [e1/63556c] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-2)
oct.-22 17:21:25.510 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 95; name: Denoise_T1 (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/06/f21f51c6fc7c4cbcbfdd9604645cc3]
oct.-22 17:21:25.512 [Task monitor] INFO  nextflow.processor.TaskProcessor - [06/f21f51] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:25.518 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:25.519 [Task submitter] INFO  nextflow.Session - [b9/bd5f85] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-2)
oct.-22 17:21:26.150 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 96; name: Denoise_T1 (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/f1/8d17376b7a00ef282dcc1419c331de]
oct.-22 17:21:26.152 [Task monitor] INFO  nextflow.processor.TaskProcessor - [f1/8d1737] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Execution is retried (3)
oct.-22 17:21:26.184 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:26.184 [Task submitter] INFO  nextflow.Session - [51/081c03] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-2)
oct.-22 17:21:26.349 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 97; name: Denoise_DWI (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/e8/38850a4bb778c1404319ebe5af9636]
oct.-22 17:21:26.350 [Task monitor] INFO  nextflow.processor.TaskProcessor - [e8/38850a] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:26.369 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:26.369 [Task submitter] INFO  nextflow.Session - [3e/397a0d] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-3)
oct.-22 17:21:26.523 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 99; name: Denoise_T1 (sub-PT001_ses-3_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/d1/21ee24e25bca86928c323b0647a177]
oct.-22 17:21:26.524 [Task monitor] INFO  nextflow.processor.TaskProcessor - [d1/21ee24] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:26.583 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:26.584 [Task submitter] INFO  nextflow.Session - [1d/08136c] Re-submitted process > Denoise_DWI (sub-PT001_ses-3_acq-3)
oct.-22 17:21:26.807 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 98; name: Denoise_T1 (sub-PT001_ses-1_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/8f/0e796734aefdcbe450db6cdaad10d3]
oct.-22 17:21:26.808 [Task monitor] INFO  nextflow.processor.TaskProcessor - [8f/0e7967] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:26.815 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:26.815 [Task submitter] INFO  nextflow.Session - [75/0b52f8] Re-submitted process > Denoise_DWI (sub-PT001_ses-2_acq-2)
oct.-22 17:21:26.817 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 100; name: Denoise_T1 (sub-PT001_ses-2_acq-1); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/95/f450f83192e33eae758c82674578dd]
oct.-22 17:21:26.817 [Task monitor] INFO  nextflow.processor.TaskProcessor - [95/f450f8] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-1)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:26.824 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:26.824 [Task submitter] INFO  nextflow.Session - [25/a90b3b] Re-submitted process > Denoise_DWI (sub-PT001_ses-1_acq-3)
oct.-22 17:21:26.999 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 101; name: Denoise_T1 (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/e1/63556c0662b28a53eb838801c30ab2]
oct.-22 17:21:27.000 [Task monitor] INFO  nextflow.processor.TaskProcessor - [e1/63556c] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:27.007 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:27.007 [Task submitter] INFO  nextflow.Session - [99/d5fc05] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-2)
oct.-22 17:21:27.075 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 102; name: Denoise_DWI (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/b9/bd5f85177ca183e0c85c9808bb8ce7]
oct.-22 17:21:27.076 [Task monitor] INFO  nextflow.processor.TaskProcessor - [b9/bd5f85] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:27.096 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:27.097 [Task submitter] INFO  nextflow.Session - [42/83e80b] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-3)
oct.-22 17:21:27.770 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 103; name: Denoise_DWI (sub-PT001_ses-1_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/51/081c0387c972ca49728369fe0fc37c]
oct.-22 17:21:27.771 [Task monitor] INFO  nextflow.processor.TaskProcessor - [51/081c03] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:27.787 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:27.787 [Task submitter] INFO  nextflow.Session - [55/9119f5] Re-submitted process > Denoise_T1 (sub-PT001_ses-2_acq-2)
oct.-22 17:21:27.978 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 104; name: Denoise_DWI (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/3e/397a0d110ff0a46b47b808eda2c7cb]
oct.-22 17:21:27.979 [Task monitor] INFO  nextflow.processor.TaskProcessor - [3e/397a0d] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:28.010 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:28.011 [Task submitter] INFO  nextflow.Session - [da/fc7182] Re-submitted process > Denoise_T1 (sub-PT001_ses-3_acq-3)
oct.-22 17:21:28.169 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 105; name: Denoise_DWI (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/1d/08136ce57edf0ec28ae95b0b7315e4]
oct.-22 17:21:28.170 [Task monitor] INFO  nextflow.processor.TaskProcessor - [1d/08136c] NOTE: Process `Denoise_DWI (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:28.175 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
oct.-22 17:21:28.176 [Task submitter] INFO  nextflow.Session - [21/42c5e7] Re-submitted process > Denoise_T1 (sub-PT001_ses-1_acq-3)
oct.-22 17:21:28.379 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 107; name: Denoise_DWI (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/25/a90b3b038e2b793626b772a1e4a602]
oct.-22 17:21:28.379 [Task monitor] INFO  nextflow.processor.TaskProcessor - [25/a90b3b] NOTE: Process `Denoise_DWI (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:28.388 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 106; name: Denoise_DWI (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/75/0b52f82ba588802ed08652f364efd3]
oct.-22 17:21:28.389 [Task monitor] INFO  nextflow.processor.TaskProcessor - [75/0b52f8] NOTE: Process `Denoise_DWI (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:28.391 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Denoise_DWI)
oct.-22 17:21:28.392 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Eddy)
oct.-22 17:21:28.392 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Topup)
oct.-22 17:21:28.392 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Eddy_Topup)
oct.-22 17:21:28.393 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Extract_B0)
oct.-22 17:21:28.394 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Bet_DWI)
oct.-22 17:21:28.394 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: N4_DWI)
oct.-22 17:21:28.394 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Crop_DWI)
oct.-22 17:21:28.395 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Normalize_DWI)
oct.-22 17:21:28.395 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Resample_DWI)
oct.-22 17:21:28.395 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Extract_DTI_Shell)
oct.-22 17:21:28.396 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Resample_B0)
oct.-22 17:21:28.396 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Extract_FODF_Shell)
oct.-22 17:21:28.397 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: DTI_Metrics)
oct.-22 17:21:28.397 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: Compute_FRF)
oct.-22 17:21:28.397 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: FODF_Metrics)
oct.-22 17:21:28.398 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: Mean_FRF)
oct.-22 17:21:28.559 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 108; name: Denoise_T1 (sub-PT001_ses-3_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/99/d5fc053639e7da7171c6623703bb5d]
oct.-22 17:21:28.560 [Task monitor] INFO  nextflow.processor.TaskProcessor - [99/d5fc05] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:28.640 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 109; name: Denoise_T1 (sub-PT001_ses-2_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/42/83e80b24adbd9205eecc5626f2ceb9]
oct.-22 17:21:28.640 [Task monitor] INFO  nextflow.processor.TaskProcessor - [42/83e80b] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:29.323 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 110; name: Denoise_T1 (sub-PT001_ses-2_acq-2); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/55/9119f5bfc0565ff7f17c3c9160841f]
oct.-22 17:21:29.324 [Task monitor] INFO  nextflow.processor.TaskProcessor - [55/9119f5] NOTE: Process `Denoise_T1 (sub-PT001_ses-2_acq-2)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:29.558 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 111; name: Denoise_T1 (sub-PT001_ses-3_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/da/fc7182b492a6130f9b11affe8be192]
oct.-22 17:21:29.559 [Task monitor] INFO  nextflow.processor.TaskProcessor - [da/fc7182] NOTE: Process `Denoise_T1 (sub-PT001_ses-3_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:29.677 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 112; name: Denoise_T1 (sub-PT001_ses-1_acq-3); status: COMPLETED; exit: 1; error: -; workDir: /netapp/vol1_homeunix/mvanhoutte/Scripts/work/21/42c5e79e4e9ee32ddc0390372b8308]
oct.-22 17:21:29.678 [Task monitor] INFO  nextflow.processor.TaskProcessor - [21/42c5e7] NOTE: Process `Denoise_T1 (sub-PT001_ses-1_acq-3)` terminated with an error exit status (1) -- Error is ignored
oct.-22 17:21:29.678 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: Denoise_T1)
oct.-22 17:21:29.679 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: N4_T1)
oct.-22 17:21:29.679 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Resample_T1)
oct.-22 17:21:29.680 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Bet_T1)
oct.-22 17:21:29.680 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Crop_T1)
oct.-22 17:21:29.680 [Actor Thread 26] DEBUG nextflow.Session - <<< barrier arrive (process: Register_T1)
oct.-22 17:21:29.680 [Actor Thread 5] DEBUG nextflow.Session - <<< barrier arrive (process: Segment_Tissues)
oct.-22 17:21:29.681 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: PFT_Maps)
oct.-22 17:21:29.681 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: Seeding_Mask)
oct.-22 17:21:29.681 [Actor Thread 41] DEBUG nextflow.Session - <<< barrier arrive (process: Tracking)
oct.-22 17:21:29.681 [main] DEBUG nextflow.Session - Session await > all process finished
oct.-22 17:21:29.777 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local)
oct.-22 17:21:29.778 [main] DEBUG nextflow.Session - Session await > all barriers passed
oct.-22 17:21:29.781 [main] INFO  nextflow.Nextflow - Pipeline completed at: Tue Oct 22 17:21:29 CEST 2019
oct.-22 17:21:29.781 [main] INFO  nextflow.Nextflow - Execution status: OK
oct.-22 17:21:29.788 [main] INFO  nextflow.Nextflow - Execution duration: 23.2s
oct.-22 17:21:29.796 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=0; failedCount=84; ignoredCount=28; cachedCount=0; succeedDuration=0ms; failedDuration=9m 40s; cachedDuration=0ms]
oct.-22 17:21:29.946 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
oct.-22 17:21:29.969 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

Could you help me to understand this issue?

Best,
Matthieu

problems lauching tractoflow on Ubuntu 22.04 Jammy

Hi,

I have a Ubuntu 22.04 desktop system with 64GB of memory and i9 intel processor. I have have tried running via singularity with the following command via a bash shell script:

NXF_VER=22.10.4 nextflow run tractoflow -r 2.4.2 --input $wkdir/dwi_preproc -profile use_cuda ABS fully_reproducible --readout 0.0708501 --run_t1_denoising false --processes 4 --run_pft_tracking false -with-singularity $pathto/scilus_1.5.0.sif

While some of the processes do run e.g. denoise dwi and prepare for topup. It will always stop running and generate the following error in the .nextflow.log file:

01:54:30.574 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 371; name: Eddy_Topup (S12); status: COMPLETED; exit: 255; error: -; workDir: $pathto/dwi_preproc/work/98/750822d4c3c955352fd33dc556cc96]

This error is repeated as it trys to rerun eddy_topup.

The same exit error 225 is also displayed in the terminal.

Could anyone help?

Thanks

Yizhou

[Bug] Tractoflow does not work with BIDS structure without fmap

It will be fixed with the new version of the container scilpy (with python 3.10).
In order to make it work without fmap users should use flat version of tractoflow

Change size of peaks nii.gz file

Hello,

I would like to use TractSeg to postprocess my peaks.nii files. However, the program expects only 3 peaks, so the .nii should be [x,y,z,9], as this is the standard from MrTrix. However, the peaks.nii file from Tractoflor contains 5 peaks, leading to a [x,y,z,15] peaks.nii file. Is there a parameter I can set within Tractoflow to only produce 3 peaks, or alternatively a way to extract the 3 biggest peaks from nii?

Thanks,
Steven