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 548864 of 905208634 bytes (0.1%, 28.5min remaining)
Downloaded 2449408 of 905208634 bytes (0.3%, 12.7min remaining)
Downloaded 4538368 of 905208634 bytes (0.5%, 10.2min remaining)
Downloaded 6848512 of 905208634 bytes (0.8%,  9.0min remaining)
Downloaded 9379840 of 905208634 bytes (1.0%,  8.1min remaining)
Downloaded 12279808 of 905208634 bytes (1.4%,  7.4min remaining)
Downloaded 15376384 of 905208634 bytes (1.7%,  6.9min remaining)
Downloaded 18882560 of 905208634 bytes (2.1%,  6.4min remaining)
Downloaded 22642688 of 905208634 bytes (2.5%,  6.0min remaining)
Downloaded 26624000 of 905208634 bytes (2.9%,  5.6min remaining)
Downloaded 31105024 of 905208634 bytes (3.4%,  5.2min remaining)
Downloaded 37224448 of 905208634 bytes (4.1%,  4.8min remaining)
Downloaded 45187072 of 905208634 bytes (5.0%,  4.2min remaining)
Downloaded 55582720 of 905208634 bytes (6.1%,  3.6min remaining)
Downloaded 68927488 of 905208634 bytes (7.6%,  3.1min remaining)
Downloaded 86302720 of 905208634 bytes (9.5%,  2.6min remaining)
Downloaded 107585536 of 905208634 bytes (11.9%,  2.1min remaining)
Downloaded 133980160 of 905208634 bytes (14.8%,  1.8min remaining)
Downloaded 166445056 of 905208634 bytes (18.4%,  1.4min remaining)
Downloaded 206422016 of 905208634 bytes (22.8%,  1.1min remaining)
Downloaded 252772352 of 905208634 bytes (27.9%,   55.1s remaining)
Downloaded 307150848 of 905208634 bytes (33.9%,   43.5s remaining)
Downloaded 368656384 of 905208634 bytes (40.7%,   34.0s remaining)
Downloaded 435781632 of 905208634 bytes (48.1%,   26.2s remaining)
Downloaded 501899264 of 905208634 bytes (55.4%,   20.4s remaining)
Downloaded 569024512 of 905208634 bytes (62.9%,   15.6s remaining)
Downloaded 629628928 of 905208634 bytes (69.6%,   12.0s remaining)
Downloaded 689315840 of 905208634 bytes (76.1%,    8.9s remaining)
Downloaded 754196480 of 905208634 bytes (83.3%,    5.9s remaining)
Downloaded 818421760 of 905208634 bytes (90.4%,    3.2s remaining)
Downloaded 885850112 of 905208634 bytes (97.9%,    0.7s remaining) ...done. (32 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]
  1%|          | 69.6k/10.7M [00:00<00:15, 673kB/s]
  3%|▎         | 366k/10.7M [00:00<00:05, 1.95MB/s]
 14%|█▍        | 1.53M/10.7M [00:00<00:01, 6.15MB/s]
 59%|█████▊    | 6.26M/10.7M [00:00<00:00, 21.6MB/s]
100%|██████████| 10.7M/10.7M [00:00<00:00, 21.8MB/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,
    )