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Genevieve Hayes edited this page Nov 24, 2022 · 8 revisions

How to use anatROIs

Prerequisite

  • You MUST read and agree to the license agreement and register with MGH before you use the software.
  • Once you get your license you can edit the example_config.json file to include your license details before you build the container. Without a license the execution of the code will fail.
  • This image is built with the Matlab MCRv97 (2019b) included. The MCR is required to run the optional Hippocampal Subfields and Brainstem Structures processing

Inputs

One of either:

  1. T1 nifti image
    -or-
  2. Already processed full freesurfer pipeline (zipped)

Optional (if the folder and file are there, the container will use them):

  • Zip file containing volumetric ROIs in MNI: they will be converted to individual subject space
    -or-
  • Zip file containing surface ROIs in fsaverage (annotations): they will be converted to individual subject space

Outputs

  1. Recon-all standard output
  2. fs.zip (this will be used for RTP-pipeline)
  3. Others

Configuration Options

Configuration for running the algorithm (and adding the license) are defined within example_config.json.

Example Local Usage

This Gear is designed to run within Flywheel, however you can run this Gear locally. To run recon-all from this image you can do the following using either Docker or Singularity:

Using Docker

docker run --rm -ti \
    -v </path/to/input/data>:/input/flywheel/v0/input/anatomical \
    -v </path/for/output/data>:/output \
    -v </path/for/example_config.json>:/flywheel/v0/config.json
    garikoitz/anatROIs:<version-tag>

Using Singularity

singularity run -e --no-home \
    --bind /scratch:/scratch \
    --bind </path/to/input/data>:/input/flywheel/v0/input/anatomical:ro \
    --bind </path/for/output/data>:/output \
    --bind </path/for/example_config.json>:/flywheel/v0/config.json
    garikoitz/anatROIs:<version-tag>

Usage Notes

  • You must mount the directory (using the -v flag in Docker, or --bind in Singularity) which contains your anatomical data (T1 nifti image) in the container at /input/flywheel/v0/input/anatomical and also mount the directory where you want your output data stored at /output, see the example above.

  • Configuration options (including the license key) must be set in the example_config.json file before building the container.

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