Comments (6)
Perfect, everything you see in this PR will be in the next release end of this week I think.
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Thank you @raniaezzo for reporting this issue. I'll try to replicate it asap and fix it if needed.
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@raniaezzo can you try with the PR #260 ? I think this should fix your issue.
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@arnaudbore Yes, thanks. It fixed the original issue which was about getting pydeface to run. However, after it completes, the output is not actually defaced when doing it through dcm2bids function.
When I run dcm2bids, the output includes:
INFO | Running: pydeface --outfile /Users/rje257/Desktop/BIDS_testing/sub-0325/ses-01/anat/sub-0325_ses-01_run-01_T1w.nii.gz /Users/rje257/Desktop/BIDS_testing/tmp_dcm2bids/sub-0325_ses-01/032_Subject_0325_anat-T1w_20221003112735.nii.gz --verbose --debug --force
. . .
(it pauses and takes a while during the defacing step)
. . .
INFO | --- dcm2bids end ---
But the output /Users/rje257/Desktop/BIDS_testing/sub-0325/ses-01/anat/sub-0325_ses-01_run-01_T1w.nii.gz is NOT defaced.
I copied the output file back into the tmp directory and re-ran the pydeface command directly (not through dcm2bids), and the defacing works.
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I fixed the issue I think you are referring. Can you check you test the PR with the latest commit.
commit 2dc01db96bcbd505ef6559e6ebffb877990582f0 (HEAD -> fix_post_op, origin/fix_post_op)
Author: Arnaud Bore <[email protected]>
Date: Mon Sep 11 17:14:15 2023 -0400
change cp to shutil copy
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Yes, that worked. Thanks!
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Related Issues (20)
- pydra-dcm2bids: Pydra tasks for dcm2bids HOT 5
- Add "run" info to files even if not duplicates HOT 1
- dcm2bids goes crazy if `--participant` contains - or _
- [feature request] always add `run-<>` label HOT 1
- Problem with dcm2bids HOT 1
- IntendedFor and Sources with only relative path to dataset root is now deprecated
- Two H1s in "How to use advanced configuration" prevent full TOC
- sidecar_changes doesn't support int / numerical objects
- Should this line be pointing to one of the sidecar files? HOT 2
- Typos in some files of the scaffold raise errors on the validator
- Creating several 3D images instead of a single 4D image. HOT 2
- New features or enh for next release
- Provide a Docker image that includes pydeface HOT 4
- [BUG] dcmbids binary
- Processing order issue ? ```"IntendedFor" No id found for 'IntendedFor' value 'XX'``` HOT 4
- KeyError: 'datatype' HOT 1
- TypeError in Acquisition.init() when running dcm2bids HOT 1
- `sidecar_changes` do not fetch all matches of the referenced description
- Error: Too many NIFTI images with the name HOT 1
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