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pBFSLab / FastCSR

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Surface generation failed. #4

Open MLGBXXX opened 1 year ago

MLGBXXX commented 1 year ago

HI author, I try to run the project with docker, but the render failed. It did not show what had happed in the error.

[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py Please cite the following paper when using FastCSR:

[INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/orig.mgz file already exists, skip this step. [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -----------------------Generate mri/filled.mgz file------------------------------- [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/filled.mgz file already exists, skip this step. [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py --------------------Generate mri/aseg.presurf.mgz file---------------------------- [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/aseg.presurf.mgz file already exists, skip this step. [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py ---------------------Generate mri/brainmask.mgz file------------------------------ [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/brainmask.mgz file already exists, skip this step. [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -------------------------Generate mri/wm.mgz file--------------------------------- [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py The mri/wm.mgz file already exists, skip this step. [INFO] 2023-08-12 03:39:35 PID: 1 pipeline.py -------------------Generate mri/?h_levelset.nii.gz file--------------------------- [INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py Levelset model regression inference completed. [INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py -------------------Generate mri/brain.finalsurfs.mgz file------------------------- [INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py The mri/brain.finalsurfs.mgz file already exists, skip this step. [INFO] 2023-08-12 03:40:50 PID: 1 pipeline.py -----------------------------Generate surface------------------------------------- [ERROR] 2023-08-12 03:41:07 PID: 1 pipeline.py Surface generation failed.

MLGBXXX commented 1 year ago

Topology Correction Traceback (most recent call last): File "/root/FastCSR/levelset2surf.py", line 106, in levelset2surf(fastcsr_subjects_dir, subj, hemi, suffix) File "/root/FastCSR/levelset2surf.py", line 57, in levelset2surf tc_ret = nighres.shape.topology_correction(img, 'signed_distance_function', File "/usr/local/lib/python3.8/dist-packages/nighres/shape/topology_correction.py", line 109, in topology_correction data = img.get_data() File "/usr/local/lib/python3.8/dist-packages/nibabel/deprecator.py", line 208, in deprecated_func raise exception(message) nibabel.deprecator.ExpiredDeprecationError: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

weiwei2027 commented 9 months ago

@MLGBXXX Hello, I’m sorry that I only saw the reply now. This seems to be a compatibility issue caused by the relatively new installed nibabel package. You can try to solve it by gradually lowering the version, or modify the code to use get_fdata() instead of get_data().