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Singularity.md

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Singularity

We host releases of the hipsta package and all required external packages as Docker images on Dockerhub. For use on HPC systems or in other cases where Docker is not preferred you can easily create a Singularity image from the Docker images.

Singularity Image Creation

For creating a singularity image from the Dockerhub just run:

cd /home/user/my_singlarity_images
singularity build hipsta-latest.sif docker://deepmi/hipsta:latest

Singularity Images are saved as .sif files. Here the /homer/user/my_singlarity_images is the path where you want your file saved. You can change deepmi/hipsta:latest with any tag provided in our Dockerhub.

If you want to use a locally available image that you created yourself, instead run:

cd /home/user/my_singlarity_images
singularity build hipsta-myimage.sif docker-daemon://hipsta:myimage

For how to create your own Docker images see our Docker guide

Singularity Image Usage

After building the Singularity image, you need to register at the FreeSurfer website (https://surfer.nmr.mgh.harvard.edu/registration.html) to acquire a valid license (for free). If you already have an existing FreeSurfer installation, you can use the license file of that installation as well.

To run the shape and thickness analysis on a given subject using the Singularity image, execute the following command (after adjusting to your particular environment):

singularity exec \
    -B /path/to/my/input/directory:/path_to_input_directory_inside_container \
    -B /path/to/my/output/directory:/path_to_output_directory_inside_container \
    -B /path/to/my/freesurfer/installation/.license:/opt/freesurfer/.license
    /home/user/my_singularity_images/hipsta.sif \
    run_hipsta \
    --filename /path_to_input_directory_inside_container/my_filename.mgz \
    --outputdir /path_to_output_directory_inside_container \
    --hemi HEMISPHERE \
    --lut LOOKUP-TABLE
  • The first two -B arguments mount your data directory and output directories into the singularity image (note that full, not relative, pathnames should be given). Inside the image, they are visible under the name following the colon (in this case /path_to_input_directory_inside_container and /path_to_output_directory_inside_container, but these can be different). From within the singularity image / container, there will be read and write access to the directories that are mounted into the image (unless specified otherwise).
  • The third -B argument mounts your freesurfer license to the FreeSurfer directory within the singularity image (/opt/freesurfer). You can use a .license or a license.txt file, which can, but does not need to, be present in your local FreeSurfer directory on your system. The version of the license should correspond to the version inside the Dockerfile that was used to create the original Docker image.
  • The next part of the command is the name of the Singularity image, which is hipsta.sif. In this example it is located in /home/user/my_singularity_images, but the specific path will likely be different on your local system.
  • For the Singularity image, we also have to explicitly specify the command that we want run, i.e. run_hipsta.
  • After that, all other flags are identical to the ones that are used for the run_hipsta program (which are explained on the main page and the help message of the program). Note that, in addition to the --filename, --hemi, --lut arguments, which are mandatory, additional arguments such as --outputdir can be specified. Also note that file- and pathnames need to correspond to the targets of the file / directory mappings within the singularity image, not to the local system. Finally, HEMISPHERE should either be lh or rh, and LOOKUP-TABLE should be freesurfer, ashs-penn_abc_3t_t2, ashs-umcutrecht_7t or a custom segmentation.