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

Note

Go to the end to download the full example code.

Quasi RAW pre-processing use case¶

Credit: A Grigis

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

# sphinx_gallery_thumbnail_path = '_static/carousel/quasiraw.jpg'

import os
import subprocess
from brainrise.datasets import MRIToyDataset

Please tune these parameters.

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

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 = ["singularity", "run", "--bind", "{0}:/data".format(DATADIR),
       "--bind", "{0}:/out".format(OUTDIR), "--home", HOMEDIR, "--cleanenv",
       SIMG,
       "brainprep", SCRIPT,
       t1w_file.replace(DATADIR, "/data"),
       mask_file.replace(DATADIR, "/data"),
       "/out",
       "--no-bids"]

You can now execute this command.

print(" ".join(cmd))

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 quasiraw /data/T1W.nii.gz /data/brainmask.nii.gz /out --no-bids

Total running time of the script: (0 minutes 0.282 seconds)

Estimated memory usage: 68 MB

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