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| '''Index''' [[Table of Contents(2)]] |
== How to Run == |
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| == How to Use == | '' Note by running the executable with no parameters will also give information on how to run the program '' |
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| Usage: ./runProject.sh <Patient File> <OPTION: DTI> |
=== 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. | Usage: ./runProject.sh <Patient File> <OPTION: DTI> |
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| === File System Requirements === | DTI is an option that allows more metrics about the FA values to be outputted based on 4 volumes |
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| Requires a subject's file to look like this: | ''''' If specific files are wanted to be used or files cannot be found, run the programs individually (read below) ''''' |
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| EXAMPLES OF THE FILE SYSTEM | === Individually === |
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| For DTI, the folder must look like this: | ==== Group by Endpoints ==== |
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| 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 |
==== 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