8.3. UKB VBM GMD Extraction

Authors: Federico Raimondo

License: BSD 3 clause

Added README.md to /github/home/nilearn_data


Dataset created in /github/home/nilearn_data/oasis1

Downloading data from https://www.nitrc.org/frs/download.php/6364/archive_dartel.tgz ...

Downloaded 147791872 of 905208634 bytes (16.3%,    5.1s remaining)
Downloaded 320290816 of 905208634 bytes (35.4%,    3.7s remaining)
Downloaded 481312768 of 905208634 bytes (53.2%,    2.6s remaining)
Downloaded 662544384 of 905208634 bytes (73.2%,    1.5s remaining)
Downloaded 845185024 of 905208634 bytes (93.4%,    0.4s remaining) ...done. (6 seconds, 0 min)
Extracting data from /github/home/nilearn_data/oasis1/7088b0bf88f5650db26e32ec3afdd589/archive_dartel.tgz..... done.
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152Lin/tpl-MNI152Lin_res-01_T1w.nii.gz

  0%|          | 0.00/10.7M [00:00<?, ?B/s]
 12%|█▏        | 1.27M/10.7M [00:00<00:00, 12.3MB/s]
 92%|█████████▏| 9.78M/10.7M [00:00<00:00, 54.5MB/s]
100%|██████████| 10.7M/10.7M [00:00<00:00, 50.3MB/s]

import tempfile

import junifer.testing.registry  # noqa: F401
from junifer.api import run


datagrabber = {
    "kind": "OasisVBMTestingDataGrabber",
}

markers = [
    {
        "name": "Schaefer1000x7_TrimMean80",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "trim_mean",
        "method_params": {"proportiontocut": 0.2},
    },
    {
        "name": "Schaefer1000x7_Mean",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "mean",
    },
    {
        "name": "Schaefer1000x7_Std",
        "kind": "ParcelAggregation",
        "parcellation": "Schaefer1000x7",
        "method": "std",
    },
]

storage = {
    "kind": "SQLiteFeatureStorage",
}

with tempfile.TemporaryDirectory() as tmpdir:
    uri = f"{tmpdir}/test.sqlite"
    storage["uri"] = uri
    run(
        workdir="/tmp",
        datagrabber=datagrabber,
        markers=markers,
        storage=storage,
    )