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== How to Use == == How to Run ==

'' Note by running the executable with no parameters will also give information on how to run the program ''

=== Full Program ===
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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. DTI is an option that allows more metrics about the FA values to be outputted based on 4 volumes
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=== File System Requirements === ''''' If specific files are wanted to be used or files cannot be found, run the programs individually (read below) '''''
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Requires a subject's file to look like this: === Individually ===
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[[attachment:Examples of Subjects]] ==== Group by Endpoints ====
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[[attachment:4 Main Folders]]

[[attachment:Within DMRI Folder]]

 *Only need FOD folder and possibly DTI folder for the FA optional flag

For DTI, the folder must look like this:

[[attachment:Within DTI Folder]]

''''' 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:

[[attachment: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.

[[attachment:U-Shape Folder]]

[[attachment: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.

[[attachment:Measures Folder]]

[[attachment:CSV Folder]]
==== Extract Surface Measurements ====

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 Run

Note by running the executable with no parameters will also give information on how to run the program

Full Program

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

DTI is an option that allows more metrics about the FA values to be outputted based on 4 volumes

If specific files are wanted to be used or files cannot be found, run the programs individually (read below)

Individually

Group by Endpoints

Extract Surface Measurements

U-Shape Bundle Analysis (last edited 2019-08-09 15:18:12 by AlexZsikla)