tutorials: ROI-based analysis

ROI-based analysis is a method to assess regional differences in brain structure based on voxelwise volume measures and average thickness measures.

Prior to running ROI-based analysis in BrainSuite Statistics toolbox (BSS), Cortical Surface Extraction and Surface/Volume Registration need to be run on your subject data. All these processes have been run for this tutorial and are available here. Please download this file and unzip this file in a convenient location, such as your desktop. It contains the folder USC2015_BrainSuiteWorkshop, in which you will find ICBM25 folder containing the necessary files to run this tutorial.

For this tutorial, we will be looking at the effect of age on ROIwise thickness in the left and right insula when controlled for sex in 25 subjects.

BSS should already be installed on your computer. If you have not done so, you can go here for download/installation.

BSS: ROI-based Analysis Tutorial

Data Preparation

This step modifies the demographics file, which contains data regarding subjects (i.e. gender, age, etc.), for analysis. It also writes out a modelspec.ini file, in which you can specify your model of interest.

  1. Open the terminal and navigate to your ICBM25 folder, located in the USC2015_BrainSuiteWorkshop directory.
    For example, in Mac:

    cd ~/Desktop/USC2015_BrainSuiteWorkshop/ICBM25
  2. On the command line, run (all in one line):
    If Mac or Linux:

    /Application/BSS/bin/bss_prepare_data_for_roi.py ~/Desktop/USC2015_BrainSuiteWorkshop/ICBM25
    ICBM_demographics.csv modelspec_skeleton_roi.ini gmthickness 500,501

    bss_prepare_data_for_roi.py will add the full paths of each *.roiwise.stats.txt into the demographics file. The usage for this script is the following (all in one line):

    <path to bss installation>/bin/bss_prepare_data_for_roi.py master_subj_dir demographics_csvmodelspec roi_measure roii_id

Model Specification

  1. The modelspec_skeleton_roi.ini describes subject and model information.
    First, change the atlas= to reflect the locations of your mri.bfc.nii.gz atlas file.
    Since we will be testing for the effect of age as main effect while controlling for sex, our full model will be Age + Sex and our null model will be Sex. These variables need to be in the demographics file as column names (case-sensitive). Type in the full model next to full model= and null model next to null model= in the [model] section. Save this file.
    Important!! The modelspec_skeleton_roi.ini can only contain either the [model] or the [measure] section but not both. So delete the entire [model] section.

Run Group Analysis

  1. Finally, run bss_roi.py in the terminal. If Mac or Linux:
    /Applications/BSS/bin/bss_roi.py modelspec_skeleton_roi.ini ~/Desktop/roi_out

Visualization of results

  1. Navigate to the roi_out folder.
  2. Open results.txt to view the results or run report.R in R.
  3. Sample file containing the results are located here.
    Sample report.R: