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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. | === Main Bundle Analysis Program === |
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| === File System Requirements === | Usage: ./bundleAnalysis.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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| [[attachment:Within DMRI Folder]] | ==== Group by Endpoints ==== |
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| *Only need FOD folder and possibly DTI folder for the FA optional flag | Usage: ./dmri_groupByEndpoints -s <streamlineFile> -i <imageFile> -d <outputDirectory> |
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| For DTI, the folder must look like this: | The program will take in a streamline file and an image file, cluster the streamlines, and output TRK files to the output directory |
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| [[attachment:Within DTI Folder]] | ==== Extract Surface Measurements ==== |
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| ''''' Please note that the file names are case sensitive for the surface and volumes ''''' | Usage: ./dmri_extractSurfaceMeasurements -i <streamlineFile(s)> -sl <Left Hemisphere Surface> -tl <Left Thickness File> -cl <Left Curvature File> -sr <Right Hemisphere Surface> -tr <Right Thickness File> -cl <Right Curvature File> -o <outputDirectory> |
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| == Output == | OPTIONAL FLAG: -fa <number of Measures> <Given Name 1> <File 1> ... <Given Name X> <File X> |
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| In the terminal, it will output all of the file names that it will be using. | The program will take in streamlines, a full brain surface with overlay files, an output directory, and possibly image files, and will output surface metrics, such as thickness and curvature as well as FA at the endpoints of the streamlines |
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| Example: | === Additional Programs === |
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| [[attachment:Terminal Output]] | ==== Change Endpoints ==== |
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| 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. | Usage: ./dmri_changeEndpoints -i <streamlineFile> -sl <Left Hemisphere Surface> -sr <Right Hemisphere Surface> -ol <Left Overlay Filename> -or <Right Overlay Filename> -itk <Itk Volume File> -fs <FS Volume File> |
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| [[attachment:U-Shape Folder]] | The program will take in two volumes, a streamline, a surface, and the names of the overlay file that will be created, and it will assign the endpoints of the streamline to the global constant assigned at the top of the program (usually a value of 1) |
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| [[attachment:Clusters Folder]] | ==== Plots ==== |
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| 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. | Usage: python3 ./dmri_plots.py <inputDirectory> <Grouping CSV> <Structure Name> |
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| [[attachment:Measures Folder]] [[attachment:CSV Folder]] |
EXPLANATION |
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
Main Bundle Analysis Program
Usage: ./bundleAnalysis.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: ./dmri_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
Extract Surface Measurements
Usage: ./dmri_extractSurfaceMeasurements -i <streamlineFile(s)> -sl <Left Hemisphere Surface> -tl <Left Thickness File> -cl <Left Curvature File> -sr <Right Hemisphere Surface> -tr <Right Thickness File> -cl <Right Curvature File> -o <outputDirectory>
OPTIONAL FLAG: -fa <number of Measures> <Given Name 1> <File 1> ... <Given Name X> <File X>
The program will take in streamlines, a full brain surface with overlay files, an output directory, and possibly image files, and will output surface metrics, such as thickness and curvature as well as FA at the endpoints of the streamlines
Additional Programs
Change Endpoints
Usage: ./dmri_changeEndpoints -i <streamlineFile> -sl <Left Hemisphere Surface> -sr <Right Hemisphere Surface> -ol <Left Overlay Filename> -or <Right Overlay Filename> -itk <Itk Volume File> -fs <FS Volume File>
The program will take in two volumes, a streamline, a surface, and the names of the overlay file that will be created, and it will assign the endpoints of the streamline to the global constant assigned at the top of the program (usually a value of 1)
Plots
Usage: python3 ./dmri_plots.py <inputDirectory> <Grouping CSV> <Structure Name>
EXPLANATION