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edickie / ciftify

The tools of the Human Connectome Project (HCP) adapted for working with non-HCP datasets
https://edickie.github.io/ciftify/
MIT License
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permission error #179

Open andraderenew opened 1 year ago

andraderenew commented 1 year ago

Dear community: I have the following error. I tried running from sudo su but the same error pops up.

ciftify_recon_all --surf-reg FS --fs-subjects-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls' --ciftify-work-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify' s25633_T1MPRAGE_1mm_reconall Traceback (most recent call last): File "/home/andraderenew/anaconda3/bin/ciftify_recon_all", line 8, in sys.exit(main()) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 1567, in main run_ciftify_recon_all(tmpdir, settings) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 123, in run_ciftify_recon_all run_default_workflow(temp_dir, settings, meshes, expected_labels, fs_version) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 155, in run_default_workflow create_cifti_subcortical_ROIs(subject.atlas_space_dir, settings, temp_dir) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 762, in create_cifti_subcortical_ROIs link_to_template_file(settings, atlas_ROIs, File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 532, in link_to_template_file os.symlink(os.path.relpath(via_path, os.path.dirname(subject_file)), PermissionError: [Errno 1] Operation not permitted: '../../../zz_templates/Atlas_ROIs.2.nii.gz' -> '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify/s25633_T1MPRAGE_1mm_reconall/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz'

edickie commented 1 year ago

It looks like your filesystem might not work well with symlinks. Try running everything with the --no-symlinks flag.

On Tue, Dec 6, 2022 at 10:37 AM andraderenew @.***> wrote:

Dear community: I have the following error. I tried running from sudo su but the same error pops up.

ciftify_recon_all --surf-reg FS --fs-subjects-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls' --ciftify-work-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify' s25633_T1MPRAGE_1mm_reconall Traceback (most recent call last): File "/home/andraderenew/anaconda3/bin/ciftify_recon_all", line 8, in sys.exit(main()) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 1567, in main run_ciftify_recon_all(tmpdir, settings) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 123, in run_ciftify_recon_all run_default_workflow(temp_dir, settings, meshes, expected_labels, fs_version) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 155, in run_default_workflow create_cifti_subcortical_ROIs(subject.atlas_space_dir, settings, temp_dir) File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 762, in create_cifti_subcortical_ROIs link_to_template_file(settings, atlas_ROIs, File "/home/andraderenew/anaconda3/lib/python3.9/site-packages/ciftify/bin/ciftify_recon_all.py", line 532, in link_to_template_file os.symlink(os.path.relpath(via_path, os.path.dirname(subject_file)), PermissionError: [Errno 1] Operation not permitted: '../../../zz_templates/Atlas_ROIs.2.nii.gz' -> '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify/s25633_T1MPRAGE_1mm_reconall/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz'

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andraderenew commented 1 year ago

sorry to ask here may be it's best if I open another thread. My question is how to use more than one cpu cores? Is there any flag to accelarate the processing? I have 8 cores and a GPU. I have seen in the docuementation it is related to parallel but I find it diffuclt to follow from the example. If there's no other way I'll have to do it.

andraderenew commented 1 year ago

I have another error.

ciftify_recon_all --surf-reg FS --fs-subjects-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls' --ciftify-work-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify' s25634_T1MPRAGE_1mm_reconall --no-symlinks --n_cpus 8 cmd: mris_convert /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify/s25634_T1MPRAGE_1mm_reconall/T1w/Native/s25634_T1MPRAGE_1mm_reconall.L.pial.native.surf.gii Failed with returncode 255 error: No such file or directory error: MRISread(/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial): could not open file error: No such file or directory error: mris_convert: could not read surface file /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial

edickie commented 1 year ago

how are your Freesurfer outputs organized - does the file /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial exist?

On Tue, Dec 6, 2022 at 2:17 PM andraderenew @.***> wrote:

I have another error.

ciftify_recon_all --surf-reg FS --fs-subjects-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls' --ciftify-work-dir '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify' s25634_T1MPRAGE_1mm_reconall --no-symlinks --n_cpus 8 cmd: mris_convert /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/ciftify/s25634_T1MPRAGE_1mm_reconall/T1w/Native/s25634_T1MPRAGE_1mm_reconall.L.pial.native.surf.gii Failed with returncode 255 error: No such file or directory error: MRISread(/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial): could not open file error: No such file or directory error: mris_convert: could not read surface file /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Freesurfer/controls/s25634_T1MPRAGE_1mm_reconall/surf/lh.pial

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andraderenew commented 1 year ago

I was surprised to verify I do have lh.pial.T1 but not lh.pial. So that must be the issue. Shall I restart recon-all? Is it a failed reconall? May be I would end up without lh.pial again I have no idea. May be the flag autorecon-pial would work.

andraderenew commented 1 year ago

I have read in freesurfer mail archive that perhaps lh.pial and lh.pialT1 are the same file? Any comments on this?

andraderenew commented 1 year ago

which version of Freesurfer am I supposed to be using? may be 7.3.2 isn't creating lh.pial but symbolic link from lh.pial to lh.pial.T1 as I am reading from freesurfer mail archive. But I'm not sure.