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dcm2niix interface doesn't list cropped files in output #3557

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mauriliogenovese opened this issue Apr 2, 2023 · 0 comments
Open

dcm2niix interface doesn't list cropped files in output #3557

mauriliogenovese opened this issue Apr 2, 2023 · 0 comments

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@mauriliogenovese
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mauriliogenovese commented Apr 2, 2023

Summary

dcm2niix supports file cropping using -x argument (crop Boolean input in nipype)

Actual behavior

the converted_files output does not include cropped files. dcm2niix interfaces intercepts filenames checking for lines starting with "Convert" in standard output, but cropping is not reported like that. This is an example:

$ dcm2niix -w 1 -b n -z y -x y -t n -m 2 y -f ref -o . -s n -v n ./
Found 368 DICOM file(s)
Image Decompression is new: please validate conversions
Resolved discrepancy between tags (0020,1002; 0021,104F; 0054,0081)
Warning: Overwriting existing file with the name ./ref
Convert 368 DICOM as ./ref (512x512x368x1)
 Cropping from slice 156 to 448 (of 512)
Conversion required 5.894715 seconds (5.894215 for core code)

Files generated by previous run are: ref.nii.gz and ref_Crop_1.nii.gz

Expected behavior

cropped files should be included in converted_files output or maybe in a separate cropped_files

@mauriliogenovese mauriliogenovese changed the title dcm2niix interfaces desn't list cropped files in output dcm2niix interface desn't list cropped files in output Apr 2, 2023
@mauriliogenovese mauriliogenovese changed the title dcm2niix interface desn't list cropped files in output dcm2niix interface doesn't list cropped files in output Apr 2, 2023
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