Group Analysis: Checking Registrations and Segmentations

The registrations segmentations for all subjects can be checked with commands in a terminal, once you have moved the current directory to the location of the files:

 [user@localhost temp]$ cd /mnt/hgfs/LinuxShare/temp

Checking Registrations 

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 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

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 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.

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   *_t1.nii.gz   *_all_fast_firstseg.nii.gz

*_t1.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.