U-Shape Bundle Analysis

Note: all of the source code can be found on the "dmri" branch on the Freesurfer Github page. The link can be found here: https://github.com/freesurfer/freesurfer/tree/dmri/anatomicuts

How to Use

Usage:

• /runProject.sh <Patient File> <OPTION: DTI>

DTI is an option that allows more metrics about the FA values to be outputted, however the required files must be in the proper location. Check file requirements below.

File System Requirements

Requires a subject's file to look like this:

attachment:Example of Subject Folders

For DTI, the folder must look like this:

EXAMPLES OF THE DTI FILE

Please note that the file names are case sensitive for the surface and volumes

== Output ==

In the terminal, it will output all of the file names that it will be using.

Example:

EXAMPLE OF TERMINAL OUTPUT

Also, within the dmri.ac file, there will be a folder named u-shape. Within that folder will contain two folders, clusters and measures. The clusters folder will contain TRK files and be named after the region that the u-shape fibers connect.

EXAMPLE OF USHAPE FOLDER AND CLUSTERS FOLDER

The measures folder will contain CSV files with the thickness and curvature at the start and end points of a streamline. If the option DTI was used, it will include the mean FA and standard deviation for the 4 files.

EXAMPLE OF THE CSV FILE, ONE WITH DTI ONE WITHOUT DTI