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Can't use --forceDcm2niix option with dcm2bids_helper #160

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SamGuay opened this issue Apr 19, 2022 · 0 comments · Fixed by #161
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Can't use --forceDcm2niix option with dcm2bids_helper #160

SamGuay opened this issue Apr 19, 2022 · 0 comments · Fixed by #161
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@SamGuay
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SamGuay commented Apr 19, 2022

If you run dcm2bids_helper once and try to run it again, you get:

(dcm2bids) sam:~/dcm2bids-tutorial/bids_project$ dcm2bids_helper -d sourcedata/dcm_qa_nih/In/20180918GE
Previous dcm2niix directory output found:
/home/sam/dcm2bids-tutorial/bids_project/tmp_dcm2bids/helper
Use --forceDcm2niix to rerun dcm2niix
Example in:
/home/sam/dcm2bids-tutorial/bids_project/tmp_dcm2bids/helper

However when you try to --forceDcm2niix, it outputs an error:

(dcm2bids) sam:~/dcm2bids-tutorial/bids_project$ dcm2bids_helper -d sourcedata/dcm_qa_nih/In/20180918GE --forceDcm2niix
usage: dcm2bids_helper [-h] -d DICOM_DIR [DICOM_DIR ...] [-o OUTPUT_DIR]
dcm2bids_helper: error: unrecognized arguments: --forceDcm2niix

The quick n dirty way solution is to rm -r tmp_dcm2bids/helper but I think it would be great to either

  1. Improve the error message so it does not mislead by proposing a flag that's not valid; or
  2. Allow the use of the --forceDcm2niix with dcm2bids_helper
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