SpinalCordPlot: Spinal Cord fMRI heatmaps

Repository containing preliminary code and example data to create heatmaps for the spinal cord.

---

Guide to this repository:

There are two scripts used to create the heatmaps. The bash shell script x.heatmapPrep requires the Spinal Cord Toolbox, AFNI, and FSL to be installed on your machine. The second script, SCheatmap.m is a MATLAB script, and requires MATLAB to be installed.

How to use

1. To test out this code, first clone or download the repository onto your machine.
2. Download this Box folder titled exampleData (or https://northwestern.box.com/s/hhao1e7n8z4h7p90uks1d4z5is4ehcl2) and add to the repository folder on your local machine.
3. Open terminal and navigate to where you stored the repository folder on your machine.
4. Run the shell script: Type zsh x.heatmapPrep -i ~/Downloads/spinalcordplot-main/exampleData/label -f ~/Downloads/spinalcordplot-main/exampleData/func.nii.gz -o heatmap_output -s into your terminal. Adjust the input path for the proper location on your computer. For this example, not including CSF is recommended. For help information, just type zsh x.heatmapPrep -h into your terminal.
5. There will be one manual step while running the shell script. An fsleyes window with a spinal cord mask will pop-up. In edit mode, erase the top and bottom slices in the mask and save / overwrite the file, then close the window.
6. Run the MATLAB script: Navigate within MATLAB to the downloaded / cloned repository folder and open the file runSCheatmap.m. Each section within this script should run the function SCheatmap(), and output various plots. Run sections individually. For help information, type help SCheatmap into the MATLAB command window.

Notes:

• Latest testing on Mac running MacOS Catalina, MATLAB 2019b, SCT 5.2.0, AFNI 21.1.01, FSL 6.0.
• Using an external monitor might alter some of the output figure aspect ratios.
• Using bash vs. zsh shells may cause terminal messages with color to appear just as text. This is a minor bug. Program will still run.

Citation:

K. J. Hemmerling and M. G. Bright, "A visualization tool for assessment of spinal cord functional magnetic resonance imaging data quality," 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2021, pp. 3391-3394, doi: 10.1109/EMBC46164.2021.9630903.