Installation

The intended use of this pipeline is through the use of Singularity or Docker image.

Note

If you are an independent researcher working on a Windows machine or a Mac, Option 2: Docker is recommended.

Option 1: Singularity

If you are new to it, start by installing Singularity following this instructions .

Then use the following command to pull the docker image as a singularity:

singularity pull docker:://inclab/hbcd_motion_postproc:<version_num>

where version_num denotes the specific version of the container. All available versions of the container can be found here. If you are unsure of which version to use, use the tag:latest.

The full usage details can be seen under the Usage section, but the basic command to run the container using Singularity is as follows:

bids_dir=/path/to/bids_dir
output_dir=/path/to/output_dir
container=/path/to/container
analysis_level=participant

singularity run -B $bids_dir:/bids \
-B $output_dir:/out \
$container /bids /out $analysis_level

where the following folder hierarchy is assumed in this case:

bids_dir/
|-- participants.tsv
|-- participants.json
|-- sub-<label>/
|   |-- sub-<label>_sessions.tsv
|   |-- sub-<label>_sessions.json
|   |-- ses-<label>/
|   |   |-- motion/
|   |   |-- sub-<label>_ses-<label>_scans.tsv
|   |   |-- sub-<label>_ses-<label>_scans.json

Option 2: Docker

Again, if you are new, start by getting Docker Desktop using this link .

If you are a Mac user, refer this website to determine the architecture of your machine (Apple silicon vs. Intel chip).

After installing Docker Desktop, run the application. This will launch the Docker Daemon and you will be able to use the docker pull command described at the top of this page.

Use the following command to pull the docker image. Again, if unsure of the version to use, use the tag: latest.

docker pull inclab/hbcd_motion_postproc:<version_num>

Building the image from the scratch

The image can be built using the Dockerfile found in the repository.

Running the container using Docker is similar to doing so with Singularity. Here is the basic command:

bids_dir=/path/to/bids_dir
output_dir=/path/to/output_dir
analysis_level=participant

docker run -it -v $bids_dir:/bids_dir \
inclab/hbcd_motion_postproc:<version_num> \
/bids_dir /output_dir $analysis_level

Both bids_dir and output_dir should be provided as absolute paths

(ex. “/Users/user1/Documents/DATA”, “/home/user1/Documents/DATA” or “C:/Documents/DATA”)