Differences between revisions 17 and 20 (spanning 3 versions)

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)

-  ⇤ ← Revision 17 as of 2019-07-30 11:18:32 → 
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+   ← Revision 20 as of 2019-07-31 08:43:55 → ⇥
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-== How to Use ==
+== How to Run ==
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-Usage:
    ./runProject.sh <Patient File> <OPTION: DTI>
+'' Note by running the executable with no parameters will also give information on how to run the 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.
+=== Full Program ===
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+Line 12:
-=== File System Requirements ===
+Usage: ./runProject.sh <Patient File> <OPTION: DTI>
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-Requires a subject's file to look like this:
+DTI is an option that allows more metrics about the FA values to be outputted based on 4 volumes
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-[[attachment:Examples of Subjects]]
+''''' If specific files are wanted to be used or files cannot be found, run the programs individually (read below) '''''
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-[[attachment:4 Main Folders]]
+=== Individually ===
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+Line 20:
-[[attachment:Within DMRI Folder]]
+==== Group by Endpoints ====
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- *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 ====