DEPRECATED: Guide to using lpba40 to calculate mean cortical thickness and surface area

DEPRECATED

This document is now deprecated in favour of the AAL and DKT parcellations built into CIVET 1.1.12+

Introduction

This tool uses the cortex labels defined by the lpba40 atlas and CIVET output files to calculate the mean cortical thickness, and total surface area at 26 regions of interest. You can find the tool and information here: https://github.com/CobraLab/lpba40-local-civet-measures

How to use lpba40 on the CIC cluster

lpba40 works in conjunction with CIVET output and a pair of atlases to calculate CT and SA. It will spit out a .csv file with values, and can optionally output labels for each subject/ROI.

To get started, create a new folder for the tool and clone the github repository.

mkdir lpba40
cd lpba40
git clone https://github.com/CobraLab/lpba40-local-civet-measures.git

You will also need to download the atlas and the flipped version from the github page and place them inside your new lpba40 folder.

By default, the tool outputs .mnc labels to a pre-defined temp directory. If you want to keep these labels, you will need to edit the .pl script with a text editor such as nano or vi. Note that this is optional, and leaving these files for a temporary directory will not affect your final output regional CT or SA values. If you wish to keep all the labels, make a directory where you would like to store them. Find the following section near the top of the file:

#Setup temp file directory
my $tmpdir = &tempdir("$me-XXXXXXXXXXX", TMPDIR => 1, CLEANUP => 1);

Comment out the second line, and add a line below defining your desired output directory for labels. You must create this directory yourself before running the script. Be sure to list the full path.

#Setup temp file directory
#my $tmpdir = &tempdir("$me-XXXXXXXXXXX", TMPDIR => 1, CLEANUP => 1);
my $tmpdir = /data/chamal/projects/raihaan/lpba40/labels;

Before running the script, you will need to load the following modules:

module load SGE-extras
module load minc-toolkit/1.0.01

Once the modules are loaded, you can run the script. It requires the location of your CIVET output files, as well as the desired location and name of the .csv output file. For example:

./get-lpba40-CT-SA.pl /path/to/CIVET/output /path/to/output/file.csv

When running this tool on the CIC cluster, you will need to create a jobfile and submit it to the queue using qbatch. To do this, you need to run the command as above, but with the following additions:

echo ./get-lpba40-CT-SA.pl /path/to/CIVET/output /path/to/output/file.csv > jobfile

This will produce a jobfile, which you can add to the queue using qbatch.

qbatch jobfile 1 72:00:00