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[user@localhost temp]$ slicesdir -p p ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz gz *_to_std_sub.nii.gz
I recommend renaming this directory to "slicesdir_T1toMNI" since the subsequent step also creates a "slicesdir" sub-directory (see second scsreenshot).
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Link to Examples of Registration Errors.
Checking Segmentations
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The first_roi_slicesdir command will create another webpage in the slicesdir subfolder with segmentations displayed on each subject's T1 image. To view a single subject's ssegmentation (Say BOB101):
[user@localhost temp]$ first_roi_slicesdir BOB101.nii.gz BOB101_all_fast_firstseg.nii.gz
If the T1 images have the suffix "_t1", the following command will create another webpage in the slicesdir subfolder with segmentations displayed on each subject's T1 image:
[user@localhost temp]$ slicesdir first_roi_slicesdir *_t1T1.nii.gz 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.
[user@localhost temp]$ first_roi_slicesdir ./allT1/*_T1.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.