ANTsSST

ANTsSST uses antsMultivariateTemplateConstruction.sh to create single subject templates (SSTs) for longitudinal data organized according to the BIDS specification. ANTsSST requires that fMRIPrep has been run on the T1w images (Note: Only tested on fMRIPrep v20.0.5).

WARNING: Make sure to only include high quality T1w images! Otherwise, your SSTs will be poor quality. Utilize FreeQC to get quality values from Freesurfer output. See the ExtraLong project quality assessment wiki for an example of how to utilize this output to filter out low-quality sessions.

Docker

Setting up

You must install Docker to use the ANTsSST Docker image.

After Docker is installed, pull the ANTsSST image by running the following command: docker pull pennbbl/antssst:0.1.0.

Typically, Docker is used on local machines and not clusters because it requires root access. If you want to run the container on a cluster, follow the Singularity instructions.

Running ANTsSST via Docker Image

Here is an example:

docker run -it --rm \
  -v /Users/kzoner/BBL/projects/ANTS/data/fmriprep/sub-93811/:/data/input/fmriprep \
  -v /Users/kzoner/BBL/projects/ANTS/data/ANTsLongitudinal/0.1.0/subjects/sub-93811:/data/output \
  -v /Users/kzoner/BBL/projects/ANTS/data/mindboggleVsBrainCOLOR_Atlases:/data/input/atlases \
  pennbbl/antssst:0.1.0 ses-PNC1 ses-PNC2 --seed 1

To the container, you must:

1. Bind the subject's fMRIPrep output directory (/Users/kzoner/BBL/projects/ANTS/data/fmriprep/sub-93811/) to the input directory in the container (/data/input/fmriprep).

2. Bind the subject's sub-directory within the overarching ANTsLongitudinal output directory (/Users/kzoner/BBL/projects/ANTS/data/ANTsLongitudinal/subjects/sub-93811) to the output directory in the container (/data/output).

3. Specify the Docker image and version. Run docker images to see if you have the correct version pulled.

4. Pass in command line arguments to the container run script. A list of sessions to process is required (ses-PNC1 ses-PNC2). Use the --help flag to print a usage message to see other available arugments.

Singularity

Setting up

You must install Singularity to use the ANTsSST Singularity image.

After Singularity is installed, pull the ANTsSST image by running the following command: singularity pull docker://pennbbl/antssst:0.1.0.

Note that Singularity does not work on Macs, and will almost surely have to be installed by a system administrator on your institution's computing cluster.

Running ANTsSST via Singularity Image

Here is an example:

singularity run --cleanenv --writable-tmpfs --containall \
  -B ~/ants_pipelines/data/fmriprep/sub-93811:/data/input/fmriprep \
  -B ~/ants_pipelines/data/ANTsLongitudinal/subjects/sub-93811:/data/output \
  -B ~/ants_pipelines/data/mindboggleVsBrainCOLOR_Atlases:/data/input/atlases \
  ~/ants_pipelines/images/antssst_0.1.0.sif ses-PNC1 ses-PNC2 --seed 1 

In your call to Singularity you should:

1. Use --cleanenv and --containall flags to specify that you do not want environment variables to leak into the container.

2. Bind the subject's fMRIPrep output directory (~/ants_pipelines/data/fmriprep/sub-93811) to the input directory in the container (/data/input/fmriprep).

3. Bind the subject's sub-directory within the overarching NTsLongitudinal output directory (~/ants_pipelines/data/ANTsLongitudinal/subjects/sub-93811) to the output directory in the container (/data/output).

4. Specify the Singularity image file.

5. Pass in command line arguments to the container run script. A list of sessions to process is required (ses-PNC1 ses-PNC2). Use the --help flag to print a usage message to see other available arugments.

Notes

1. For details on how ANTsSST was utilized for the ExtraLong project (all longitudinal T1w data in the BBL), see this wiki.