MIC-DKFZ
Apply TractSeg to the study specific population template using the peaks of the spherical harmonic function at each voxel as input
Hi, I want to apply TractSeg to the study specific population template using the peaks of the spherical harmonic function at each voxel as input. I have peaks.nii.gz after running this command: sh2peaks wmfod_template_MNI.mif peaks.nii.gz But, when I try to run the following command, I get the following error:
TractSeg -i peaks.nii.gz -o template/tract_segmentation/ --output_type tract_segmentation
Error: Loading weights from: /home/gha/.tractseg/pretrained_weights_tract_segmentation_v3.npz Downloading pretrained weights (~140MB) ... Traceback (most recent call last): File "/home/gha/miniconda3/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn conn = connection.create_connection( File "/home/gha/miniconda3/lib/python3.9/site-packages/urllib3/util/connection.py", line 95, in create_connection raise err . . . . . raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='zenodo.org', port=443): Max retries exceeded with url: /record/3518348/files/best_weights_ep220.npz?download=1 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f7750f9c8b0>: Failed to establish a new connection: [Errno 111] Connection refused'))
Thanks in advance for your help
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.
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'
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
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
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.
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?
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