SynthSeg (and freesurfer-dev)

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Hi all,

The CBS server now has SynthSeg (https://github.com/BBillot/SynthSeg) installed via the latest dev version of freesurfer.

It performs whole brain segmentation (e.g. freesurfer aseg) agnostic to contrast or resolution. Give it a try, it takes only ~3-4 minutes to run on CBS Heavy (12 threads). Could be useful if you have clinical or low-resolution scans you need to segment.

You can use it as follows:

module load freesurfer/dev-20220215 

mri_synthseg
USAGE
    mri_synthseg [options]

DESCRIPTION
    SynthSeg

OPTIONAL ARGUMENTS
    --i  I
        Image(s) to segment. Can be a path to an image or to a folder.

    --o  O
        Segmentation output(s). Must be a folder if --i designates a folder.

    --post  POST
        (optional) Posteriors output(s). Must be a folder if --i designates a
        folder.

    --resample  RESAMPLE
        (optional) Resampled image(s). Must be a folder if --i designates a
        folder.

    --vol  VOL
        (optional) Output CSV file with volumes for all structures and
        subjects.

    --crop  INT [INT ...]
        (optional) Size of 3D patches to analyse. Default is 192.

    --threads  INT
        (optional) Number of cores to be used. Default is 1.

    --cpu
        (optional) Enforce running with CPU rather than GPU.