ScLimbic

Overview

ScLimbic provides a deep learning tool, mri_sclimbic_seg, to automatically segment several subcorical limbic structures from T1-weighted images (“SC” = subcortical). The structures are shown in the figure below (note: anterior commissure is only present for reference reasons).

Version 2021-07-25 is installed on the CSF.

Restrictions on use

We have restricted access to this application to only those people with access to FreeSurfer. Hence you should read the Restrictions on Use section of the FreeSurfer page and follow the instructions there to request access to FreeSurfer. You will not be able to run ScLimbic if you do not yet have access to FreeSurfer.

The authors of this software also state that those using this toolbox should cite: “A Deep Learning Toolbox for Automatic Segmentation of Subcortical Limbic Structures from MRI Images. Greve, DN, Billot, B, Cordero, D, Hoopes, A, Hoffmann, M, Dalca, A, Fischl, B, Iglesias, JE, Augustinack, JC. Accepted. Neuroimage 2021. 10.1016/j.neuroimage.2021.118610. PMID: 34571161.” https://pubmed.ncbi.nlm.nih.gov/34571161. PDF Available here.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

# Please note: you must not have any freesurfer modulefiles loaded to use this modulefile!
module load apps/binapps/sclimbic/20210725

Running the application

Please do not run mri_sclimbic_seg or freeview on the login node. Jobs should be submitted to the compute nodes via batch.

You may run mri_sclimbic_seg --help to see a list of command-line flags that you may wish to use when writing your jobscripts.

Running ScLimbic and FreeSurfer

It is not possible to load both a freesurfer modulefile and a sclimbic modulefile.

If you wish to run both apps in the same jobscript, you should load one, run the app, then unload that modulefile and load the next. For example

#!/bin/bash
#$ -cwd

# This will set SUBJECTS_DIR to ~/scratch/subjects
module load apps/binapps/freesurfer/7.4.1
freesurfer commands

# Unload all modulefiles
module purge

# Note that this will also set SUBJECTS_DIR to ~/scratch/subjects if you've not already set it
module load apps/binapps/sclimbic/20210725
sclimibic commands
            #
            # See below for a basic command-line

Sample Volume

The installation comes with the bert.t1.mgz sample volume, which can be found at $SCLIMBICDIR/bert.t1.mgz after loading the modulefile.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

# Please note, you CANNOT have any freesurfer modulefiles loaded at this point.
module load apps/binapps/sclimbic/20210725

mri_sclimbic_seg --i input_vol.mgz --o output_vol.mgz
  #
  # See the ScLimbic website for more command-lines

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
#$ -pe smp.pe 4     # Number of cores (2--32)
                    # NO -V line - we load modulefiles in the jobscript

# Please note, you CANNOT have any freesurfer modulefiles loaded at this point.
module load apps/binapps/sclimbic/20210725

mri_sclimbic_seg --threads $NSLOTS --i input_vol.mgz --o output_vol.mgz
  #
  # See the ScLimbic website for more command-lines                                        #

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Using the freeview viewer

This should be run in an interactive session, which will run the app on a compute node but display it on your laptop/PC as follows:

# On the CSF login node:
module load apps/binapps/sclimbic/20210725
cd ~/scratch/where/your/volumes/are
qrsh -l short -cwd -V freeview vol.mgz

Further info

• ScLimbic website which lists more command-line options for the tool.

Updates

None.