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: ROI-based Analysis Tutorial
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.
- Open the terminal and navigate to your
ICBM25folder, located in the
For example, in Mac:cd ~/Desktop/USC2015_BrainSuiteWorkshop/ICBM25
- 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.pywill add the full paths of each
*.roiwise.stats.txtinto 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
modelspec_skeleton_roi.inidescribes subject and model information.
First, change the
atlas=to reflect the locations of your
Since we will be testing for the effect of age as main effect while controlling for sex, our full model will be
Age + Sexand 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
Run Group Analysis
- Finally, run
bss_roi.pyin the terminal. If Mac or Linux:/Applications/BSS/bin/bss_roi.py modelspec_skeleton_roi.ini ~/Desktop/roi_out
Visualization of results
- Navigate to the
results.txtto view the results or run
Sample file containing the results are located here.