SKERI :: Brain imaging

We currently use a combination of the Stanford mrLoadRet/mrGray MR analysis package and the Oxford group's FSL (pronounced "fossil") toolkit.

We do not currently use SPM,Freesurfer, Brainvoyager,CARET/SureFit or AFNI. But we can often translate our data to and from those packages if need be and they will be installed on request.

The Psych Toolbox running on Mac OS9 or Windows is an excellent choice. We access it through a high-level toolbox called "ExptTools" that can be used to make fMRI stimuli.

Many of the software tools you need are stored centrally on the SKI MRI server "Darwin".

Under windows, browse to "Darwin" in the MRI workgroup and map the shared drive "MRI" to your windows "X:" drive. You will need to login as

login: MRI (all capitals)

password: bold (all lowercase)

This drive contains functional and anatomical MR data as well as the analysis toolbox. You may need to add some of the toolbox sub-directories to your Matlab path.

The standard Matlab fMRI toolboxes should work under Matlab 6 on OSX but we have never tested them. Matlab 5.x is not supported on any platform. The segmentation program "mrGray" is Windows only

Darwin is sharing the directory 'MRI' via appletalk. Login and password are the same as for MS Windows.

Stanford tool can be run under Matlab 6 on Linux. Users of the Brain Imaging Facility are encouraged to run analyses directly on the server using remote X terminals thereby gaining rapid access to the data stored on the RAID array. A login name and password will be supplied on request.