permission error

[andraderenew]

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]

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' — Reply to this email directly, view it on GitHub <#179>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEXT5SCGENJ3B3NSGTY6FTWL5MSNANCNFSM6AAAAAASVU3MB4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[andraderenew]

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]

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]

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 — Reply to this email directly, view it on GitHub <#179 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADEXT5W35CJA5PA3R4PUNXTWL6GMFANCNFSM6AAAAAASVU3MB4> . You are receiving this because you commented.Message ID: ***@***.***>

[andraderenew]

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]

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

[andraderenew]

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.