Apply TractSeg to the study specific population template using the peaks of the spherical harmonic function at each voxel as input about tractseg

[wasserth]

The code is having problems downloading the model weights from zenodo. Sometimes zenodo is having download issues. I would suggest to try it again another time and/or from another internet network.

[Nassim3235]

Thanks a lot! I fixed the problem. The following commands runned correctly:
TractSeg -i peaks.nii.gz -o template/tract_segmentation/ --output_type tract_segmentation
TractSeg -i peaks.nii.gz -o template/endings_segmentation/ --output_type endings_segmentation

But, when I try to run "TractSeg -i peaks.nii.gz -o template/TOM/ --output_type TOM" , There is no file in TOM folder and I get the following error:

Error:

Loading weights from: /home/gha/.tractseg/pretrained_weights_peak_regression_part1_v2.npz
100%|█████████████████████████████████████████| 144/144 [00:22<00:00, 6.44it/s]
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/gha/miniconda3/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'template/TOM/bundle_segmentations/AF_left.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 428, in _process_worker
r = call_item()
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 275, in call
return self.fn(*self.args, **self.kwargs)
.
.
.
.
FileNotFoundError: No such file or no access: 'template/TOM/bundle_segmentations/AF_left.nii.gz'

[wasserth]

Is this the complete error message? There seems to be missing something.

[Nassim3235]

This is the complete error message:

TractSeg -i peaks.nii.gz -o template/TOM/ --output_type TOM

Loading weights from: /home/gha/.tractseg/pretrained_weights_peak_regression_part1_v2.npz
Downloading pretrained weights (~140MB) ...
downloaded in 913.93s
100%|████████████████████████████████████████| 144/144 [00:23<00:00, 6.24it/s]
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/gha/miniconda3/lib/python3.9/site-packages/nibabel/loadsave.py", line 42, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: 'template/TOM/bundle_segmentations/AF_left.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 428, in _process_worker
r = call_item()
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 275, in call
return self.fn(*self.args, **self.kwargs)
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 620, in call
return self.func(*args, **kwargs)
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/parallel.py", line 288, in call
return [func(*args, **kwargs)
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/parallel.py", line 288, in
return [func(*args, **kwargs)
File "/home/gha/miniconda3/lib/python3.9/site-packages/tractseg/libs/peak_utils.py", line 263, in _process_bundle
img = nib.load(join(tract_seg_path, bundle + ".nii.gz"))
File "/home/gha/miniconda3/lib/python3.9/site-packages/nibabel/loadsave.py", line 44, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: 'template/TOM/bundle_segmentations/AF_left.nii.gz'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/gha/miniconda3/bin/TractSeg", line 420, in
main()
File "/home/gha/miniconda3/bin/TractSeg", line 325, in main
seg = run_tractseg(data, args.output_type,
File "/home/gha/miniconda3/lib/python3.9/site-packages/tractseg/python_api.py", line 240, in run_tractseg
seg = peak_utils.mask_and_normalize_peaks(seg, tract_segmentations_path,
File "/home/gha/miniconda3/lib/python3.9/site-packages/tractseg/libs/peak_utils.py", line 271, in mask_and_normalize_peaks
results_peaks = Parallel(n_jobs=nr_cpus)(delayed(_process_bundle)(idx, bundle)
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/parallel.py", line 1098, in call
self.retrieve()
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/parallel.py", line 975, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/home/gha/miniconda3/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 567, in wrap_future_result
return future.result(timeout=timeout)
File "/home/gha/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 445, in result
return self.__get_result()
File "/home/gha/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 390, in __get_result
raise self._exception
FileNotFoundError: No such file or no access: 'template/TOM/bundle_segmentations/AF_left.nii.gz'

[wasserth]

For the previous commands (output type tract_segmentation and endings_segmentations) you have to specify the same output folder. And for output_type TOM as well. The correct subfolders are automatically generated. Just do it the same way as it is stated in the documentation.

[Nassim3235]

Problem solved. Thank you very much for your help.

[yutinghe99]

Hi,
I met the same problem as yours, could you please tell me how did you solve the Failed to establish a new connection: [Errno 111] Connection refused'))? Just changed the internet network?

[Nassim3235]

Hi,
Yes, we just changed the internet network.

[yutinghe99]

Thanks! I solved the problem. I also try to apply TractSeg to the study specific population template. I've done whole brain fixel-based analysis according to the MRtrix3 document. And I got some significant FC, FD, FDC fixels between 3 of my groups. Now I would like to label those tracts which have significant fixels. I followed this scripts https://osf.io/9ch6a, ran the following commands
sh2peaks wmfod_template_MNI.mif peaks.nii.gz TractSeg -i peaks.nii.gz -o tractseg/ --output_type tract_segmentation TractSeg -i peaks.nii.gz -o tractseg/ --output_type endings_segmentation TractSeg -i peaks.nii.gz -o tractseg/ --output_type TOM Tracking -i peaks.nii.gz -o tractseg/ --tracking_format tck --nr_fibers 10000

The given scripts is an Tract-of-interest analysis, I"d to do whole brain analysis, and I want to know what's the next step according to my goal?

Seems you are also doing the FBA, I would appreciate it if you could give me some guidance.

Yuting