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[user@localhost temp]$ first_roi_slicesdir *_t1T1.nii.gz *_all_fast_firstseg.nii.gz
*_t1T1.nii.gz is the list of T1 images, and *_all_fast_firstseg.nii.gz is the list of segmentations. You could also specify these file by file.
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[user@localhost temp]$ first_roi_slicesdir ./allT1/*_t1T1.nii.gz *_all_fast_firstseg.nii.gz
To quickly copy all T1's, sort by file size; they should then be listed together, and easier to select all at once and copy.
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