Package that provides tools for brain MRI Deep Learning pre-processing.

Note

Go to the end to download the full example code.

FreeSurfer pre-processing use case¶

Credit: A Grigis

Example on how to run the FreeSurfer pre-processing using the brainprep Singularity container.

# sphinx_gallery_thumbnail_path = '_static/carousel/freesurfer.png'

import os
import subprocess
from brainrise.datasets import MRIToyDataset

Please tune these parameters: not that you need a valid FreeSurfer license.

DATADIR = "/tmp/brainprep-data"
OUTDIR = "/tmp/brainprep-out"
HOMEDIR = "/tmp/brainprep-home"
SCRIPT = "fsreconall"
SIMG = "/volatile/nsap/brainprep/anat/brainprep-anat-latest.simg"
FS_LICENSE = "/out/license.txt"

for path in (DATADIR, OUTDIR, HOMEDIR):
    if not os.path.isdir(path):
        os.mkdir(path)
dataset = MRIToyDataset(root=DATADIR)
t1w_file = os.path.join(DATADIR, os.path.basename(MRIToyDataset.t1w_url))
mask_file = os.path.join(DATADIR, os.path.basename(MRIToyDataset.mask_url))
cmd = ["SINGULARITYENV_FS_LICENSE={0}".format(FS_LICENSE),
       "singularity", "run", "--bind", "{0}:/data".format(DATADIR),
       "--bind", "{0}:/out".format(OUTDIR), "--home", HOMEDIR, "--cleanenv",
       SIMG,
       "brainprep", SCRIPT,
       "sub-test",
       t1w_file.replace(DATADIR, "/data"),
       "/out"]

You can now execute this command.

print(" ".join(cmd))

SINGULARITYENV_FS_LICENSE=/out/license.txt singularity run --bind /tmp/brainprep-data:/data --bind /tmp/brainprep-out:/out --home /tmp/brainprep-home --cleanenv /volatile/nsap/brainprep/anat/brainprep-anat-latest.simg brainprep fsreconall sub-test /data/T1W.nii.gz /out

Total running time of the script: (0 minutes 0.280 seconds)

Estimated memory usage: 68 MB

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