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Single_Subject_Grey_Matter_Networks

Matlab scripts that extract single subject grey matter networks from grey matter segmented T1 weighted images % READ_ME.txt: About contents Extract_individual_GM_networks % % Author: Betty Tijms, 2012. Version 20150902

% UPDATE NOTE

% The batch_extract_networks file is altered to ensure alignment with MNI space. Please use the scripts from the folder with version number 20150902

General:

Note that these scripts require the NIFTI matlab toolbox: This can be downloaded from http://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image Don't forget to add the path to this toolbox in Matlab.

Please check scripts for * --- ADJUST FOLLOWING ---* to adjust path & file names in the script. Please keep the slahses as indicated.

Extract_individual_GM_networks contains:

  1. create_cube_templates.m This script contains the templates to extract the regions of interest (the cubes) from grey matter. 2.batch_extract_networks.m: This matlab script extracts individual grey matter networks from grey matter segmentations. *Input: c1 or p1 files from SPM5/SPM8/VBM5/VBM8 or pve_1 from FSL (grey matter partial volume estimates) --> names of these stored in a .txt file *It uses functions from the folder 'functions' *It is dependent on: - Matlab 7 or higher: The script is designed to work with single precision, which is unavailable in earlier versions of Matlab. - SPM5 or SPM8 functions --> make sure the path to this software is added to Matlab - create_cube_templates.m 4.example_file_withscannames.txt: Example text file that need to contain the paths+names of the grey matter segmentations. 3.Functions: This folder contains matlab functions that are used by 'batch_extract_networks.m' . No adjustment of these files is needed.

INSTRUCTIONS

  1. The file create_cube_templates.m needs to be run just once: a. Go to the directory where you have write permissions b. Run create_cube_templates: This will create the directory 'bl_ind' which contains all possible ways to extract 3 x 3 x 3 voxel cubes from a 91 x 109 x 91 image. You will have to add this path in to the script batch_extract_networks.m 2 Create a text file that contains the names including the full path of the grey matter segmenations --> like the example in example_file_withscannames.txt
  2. Adjust batch_extract_networks.m --> between lines 40 and 60
  3. Run the script.

When you use this toolbox please provide the version number and cite the following paper: Tijms, BM, Series, P, Willshaw, DJ, & Lawrie, SM. 2012. Similarity-Based Extraction of Individual Networks from Gray Matter MRI Scans. Cerebral cortex, 22, 1530-1541.

If any problems/questions arise please contact me: b.tijms@vumc.nl or betty.tijms@gmail.com