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Link to Examples of Registration Errors.

Checking Segmentations

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]$ 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.

If your T1 images are not distinguished with a suffix, create a new directory and copy the T1 files there, and the _. You can then specify the location of the T1 files; for example, if you have copied all T1 files to a sub-directory "allT1", the following command will work:

[user@localhost temp]$ first_roi_slicesdir   ./allT1/*_T1.nii.gz   *_all_fast_firstseg.nii.gz

files. You may need to rename the T1 files, or enter them one at a time

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.