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sct-pipeline / spine-park

Pipeline for multicontrast analysis in PD patients
MIT License
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DWI folder not found #43

Closed Kaonashi22 closed 3 months ago

Kaonashi22 commented 3 months ago

I got this error while running the new script version: line 261: cd: sub-AM267/dwi/: No such file or directory err.batch_processing_sub-AM267.log

jcohenadad commented 3 months ago

Interesting. The dwi/ folder definitely exists:

SYSTEM INFORMATION
------------------
SCT info:
- version: git-master-9e1f65b86902cb237d5f79058a4623eed2d2c8eb
- path: /export02/data/lydiac/spinalcordtoolbox
OS: linux (Linux-5.15.115-i686-64-smp-x86_64-with-glibc2.31)
CPU cores: Available: 12, Used by ITK functions: 1
RAM: Total: 31991MB, Used: 8095MB, Available: 22917MB
sending incremental file list
sub-AM267/
sub-AM267/anat/
sub-AM267/anat/sub-AM267_T1map.json
sub-AM267/anat/sub-AM267_T1map.nii.gz
sub-AM267/anat/sub-AM267_T2.json
sub-AM267/anat/sub-AM267_T2.nii.gz
sub-AM267/anat/sub-AM267_UNIT1.json
sub-AM267/anat/sub-AM267_UNIT1.nii.gz
sub-AM267/anat/sub-AM267_mt-off_MTS.json
sub-AM267/anat/sub-AM267_mt-off_MTS.nii.gz
sub-AM267/anat/sub-AM267_mt-on_MTS.json
sub-AM267/anat/sub-AM267_mt-on_MTS.nii.gz
sub-AM267/dwi/
sub-AM267/dwi/sub-AM267_chunk-1_DWI.bval
sub-AM267/dwi/sub-AM267_chunk-1_DWI.bvec
sub-AM267/dwi/sub-AM267_chunk-1_DWI.json
sub-AM267/dwi/sub-AM267_chunk-1_DWI.nii.gz
sub-AM267/dwi/sub-AM267_chunk-2_DWI.bval
sub-AM267/dwi/sub-AM267_chunk-2_DWI.bvec
sub-AM267/dwi/sub-AM267_chunk-2_DWI.json
sub-AM267/dwi/sub-AM267_chunk-2_DWI.nii.gz
sub-AM267/dwi/sub-AM267_chunk-3_DWI.bval
sub-AM267/dwi/sub-AM267_chunk-3_DWI.bvec
sub-AM267/dwi/sub-AM267_chunk-3_DWI.json
sub-AM267/dwi/sub-AM267_chunk-3_DWI.nii.gz

I'm running the script across 14 subjects to see if I get an error. If I don't you can send me this subject to see if there is something particular with that subject that is causing the error.

Kaonashi22 commented 3 months ago

I got the error with the three first subjects, then I stopped the pipeline. Indeed, there is a dwi folder... I'll send you these subjects

From: Julien Cohen-Adad @.> Sent: July 2, 2024 12:33 To: sct-pipeline/spine-park @.> Cc: Lydia Chougar, Dr @.>; Author @.> Subject: Re: [sct-pipeline/spine-park] DWI folder not found (Issue #43)

Interesting. The dwi/ folder definitely exists:

SYSTEM INFORMATION

SCT info:

I'm running the script across 14 subjects to see if I get an error. If I don't you can send me this subject to see if there is something particular with that subject that is causing the error.

— Reply to this email directly, view it on GitHubhttps://github.com/sct-pipeline/spine-park/issues/43#issuecomment-2203784759, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFCFJYR5QPAS246X73EDEU3ZKLI65AVCNFSM6AAAAABKHUXWJ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBTG44DINZVHE. You are receiving this because you authored the thread.Message ID: @.***>