...
The segmentations are based on a priori templates in a standard space, so the images must be successfully registered to the template space for FIRST to work. This command will create a subdirectory sub-directory "slicesdir" which will contain a webpage visualizing each subject's registration:
[user@localhost temp]$ slicesdir -p ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz *_to_std_sub.nii.gz Open
I recommend renaming this directory to "slicesdir_T1toMNI" since the subsequent step also creates a "slicesdir" sub-directory (see second scsreenshot).
Open the "index" web page to view:
On the webpage, each subject's registered image (*_to_std_sub.nii.gz) will be displayed in sagittal, coronal, and axial views, with a red outline showing the edges from of the MNI152_T1_1mm standard brain. Open this webpage in any web browser. Check the User Guide for instructions on how to correct registrations.
Registration Errors
Checking Segmentations
This command will create another webpage in the slicesdir subfolder with segmentations displayed on each subject's T1 image:
...