Gray Matter Segmentator

This repository contains a Gray Matter(GM) segmentator implementation for the MATLAB Platform based on SPM12 and CAT12. This tool was designed specifically for the preprocessing of the images for the Diagonal Sulcus Dectection repository. All credits to the creators of those amazing toolboxes.

Content

1. Installation
   • Standalone Version
   • Matlab Platform
2. How to run
3. Compile Standalone

Installation

Standalone Version

1. Download MATLAB Runtime version 9.5 (R2018b) from the official site for your specific SO (Windows, Linux, Mac).
2. Install the "MCR_R2018b" file downloaded.
3. If you are using Windows, download the standalone version. Otherwise, compile it for your system following the steps described in the Compile Standalone section.

Matlab Platform

1. Download and install Matlab 9.5 Matlab R2018b (Recommended)
2. Download and install SPM12 v7771 addon for Matlab.
3. Download and install CAT12.9 (r2560) toolbox for SPM.

For more information about how to install those complements, please refer to the official website of SPM and CAT12

How to run

1. In the Standalone version, execute SegmentGM.exe.

   In the Matlab Platform, open run_segment_gm.m and run it.

2. Execute SegmentGM.exe and wait it to load.

3. A dialog box will pop out to select the nifti images that you want to segment.

4. Results will be placed in a folder called mri, located alongside the input images. GM segments will be named as the input images with the wp1 prefix.

Notes

• Input images can be in .nii and .nii.gz format.
• It takes aproximately 10~15min to process each image.
• The processing is CPU intensive.
• You can run several instances of the segmentator if you want to do it more quickly, however keep in mind that is going to consume more CPU and memory RAM.
• Terminal outputs will be stored in the output.txt file or the individual ones in the report folder

Compile Standalone

As a prerequisite, follow the instructions for installation in the Matlab Platform subsection.

In order to compile the GM segmentator, follow this steps:

1. Clone this repository.
2. (Optional) Download 7Zip standalone version for your SO and extract the content inside the provided 7zip folder.
3. Open the script compile_segment_gm.m in MATLAB and run it.
4. The compiled version will be located in the compiled folder.