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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 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 | Usage: ./groupByEndpoints -s <streamlineFile> -i <imageFile> -d <outputDirectory> |
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| ''''' Please note that the file names are case sensitive for the surface and volumes ''''' | The program will take in a streamline file and an image file, cluster the streamlines, and output TRK files to the output directory ==== 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
Usage: ./groupByEndpoints -s <streamlineFile> -i <imageFile> -d <outputDirectory>
The program will take in a streamline file and an image file, cluster the streamlines, and output TRK files to the output directory