MartyCole
commented
5 months ago Sometimes Freesurfer's recon-all command fails to create surfaces. Check the subjects that are failing, do they have surfaces from Freesurfer? If not, I suggest looking at the pial and white vomumes for errors in the t1_freesurfer folder of the problematic subjects. See: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData for more information
I am using SBCI to process a batch of data. The pipeline has same error when processing a few subjects. The error may related to the surface calculation using vtk package. I am not sure if this error happened because of previous steps or minimal preprocessing issue.
The error is from sbci_step2_prepare_set.sh
Traceback (most recent call last): File "/home/ywang330/.conda/envs/sbci/bin/scil_surface_from_volume.py", line 7, in <module> exec(compile(f.read(), __file__, 'exec')) File "/gpfs/fs1/home/ywang330/scilpy_set/scripts/scil_surface_from_volume.py", line 144, in <module> main() File "/gpfs/fs1/home/ywang330/scilpy_set/scripts/scil_surface_from_volume.py", line 140, in main mesh.save(args.out_surface) File "/home/ywang330/.conda/envs/sbci/lib/python2.7/site-packages/trimeshpy/trimesh_vtk.py", line 334, in save self.update() File "/home/ywang330/.conda/envs/sbci/lib/python2.7/site-packages/trimeshpy/trimesh_vtk.py", line 180, in update self.update_polydata() File "/home/ywang330/.conda/envs/sbci/lib/python2.7/site-packages/trimeshpy/trimesh_vtk.py", line 79, in update_polydata self.set_polydata_triangles(self.get_triangles()) File "/home/ywang330/.conda/envs/sbci/lib/python2.7/site-packages/trimeshpy/trimesh_vtk.py", line 90, in set_polydata_triangles np.c_[np.ones(len(triangles)).astype(np.int) * 3, triangles]) File "/home/ywang330/.conda/envs/sbci/lib/python2.7/site-packages/numpy/core/shape_base.py", line 340, in hstack return _nx.concatenate(arrs, 1) ValueError: need at least one array to concatenateHere is the sbci_step2_prepare_set.sh scrip:
Please let me know if I need to provide more info. Thank you!