8.4. Computer Parcel Aggregation.

This example uses the ParcelAggregation marker to compute the mean of each parcel using the Schaefer parcellations (100 rois, 7 Yeo networks) for both 3D and 4D NIfTI.

Authors: Federico Raimondo, Synchon Mandal

License: BSD 3 clause

from junifer.testing.datagrabbers import (
    OasisVBMTestingDataGrabber,
    SPMAuditoryTestingDataGrabber,
)
from junifer.datareader import DefaultDataReader
from junifer.markers import ParcelAggregation
from junifer.utils import configure_logging

Set the logging level to info to see extra information

configure_logging(level="INFO")

/__w/junifer/junifer/junifer/utils/logging.py:193: UserWarning: The '__version__' attribute is deprecated and will be removed in MarkupSafe 3.1. Use feature detection, or `importlib.metadata.version("markupsafe")`, instead.
  vstring = str(getattr(module, "__version__", None))
2025-01-27 11:17:43,551 - JUNIFER - INFO - ===== Lib Versions =====
2025-01-27 11:17:43,551 - JUNIFER - INFO - numpy: 1.26.4
2025-01-27 11:17:43,551 - JUNIFER - INFO - scipy: 1.15.0
2025-01-27 11:17:43,551 - JUNIFER - INFO - pandas: 2.1.4
2025-01-27 11:17:43,551 - JUNIFER - INFO - nilearn: 0.10.4
2025-01-27 11:17:43,551 - JUNIFER - INFO - nibabel: 5.3.2
2025-01-27 11:17:43,551 - JUNIFER - INFO - junifer: 0.0.6.dev450
2025-01-27 11:17:43,551 - JUNIFER - INFO - ========================

Perform parcel aggregation on VBM GM data (3D) from OASIS dataset

with OasisVBMTestingDataGrabber() as dg:
    # Get the first element
    element = dg.get_elements()[0]
    # Read the element
    element_data = DefaultDataReader().fit_transform(dg[element])
    # Initialize marker
    marker = ParcelAggregation(parcellation="Schaefer100x7", method="mean")
    # Compute feature
    feature = marker.fit_transform(element_data)
    # Print the output
    print(feature.keys())
    print(feature["VBM_GM"]["aggregation"]["data"].shape)  # Shape is (1 x parcels)

2025-01-27 11:17:43,556 - JUNIFER - INFO - Getting element sub-01
2025-01-27 11:17:43,557 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-01-27 11:17:43,557 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-01-27 11:17:43,558 - JUNIFER - INFO - Computing VBM_GM
2025-01-27 11:17:43,558 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:17:43,558 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:17:43,558 - JUNIFER - INFO -      resolution: None
2025-01-27 11:17:43,558 - JUNIFER - INFO -      n_rois: 100
2025-01-27 11:17:43,558 - JUNIFER - INFO -      yeo_networks: 7
2025-01-27 11:17:43,558 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:17:46,165 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:17:48,103 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:17:48,604 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_55cba7c8-dca0-11ef-bd11-0242ac120002b5wir_3r/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_55cba7c8-dca0-11ef-bd11-0242ac120002b5wir_3r/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_55cba7c8-dca0-11ef-bd11-0242ac120002b5wir_3r/parcellation_warped.nii.gz
2025-01-27 11:17:54,882 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2025-01-27 11:17:56,102 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['VBM_GM'])
(1, 100)

Perform parcel aggregation on BOLD data (4D) from SPM Auditory dataset

with SPMAuditoryTestingDataGrabber() as dg:
    # Get the first element
    element = dg.get_elements()[0]
    # Read the element
    element_data = DefaultDataReader().fit_transform(dg[element])
    # Initialize marker
    marker = ParcelAggregation(
        parcellation="Schaefer100x7", method="mean", on="BOLD"
    )
    # Compute feature
    feature = marker.fit_transform(element_data)
    # Print the output
    print(feature.keys())
    print(feature["BOLD"]["aggregation"]["data"].shape)  # Shape is (timepoints x parcels)

2025-01-27 11:17:56,103 - JUNIFER - INFO - Getting element sub001

Dataset created in /github/home/nilearn_data/spm_auditory

Data absent, downloading...
Downloading data from https://www.fil.ion.ucl.ac.uk/spm/download/data/MoAEpilot/MoAEpilot.zip ...

Downloaded 3317760 of 34212021 bytes (9.7%,    9.5s remaining)
Downloaded 8404992 of 34212021 bytes (24.6%,    6.2s remaining)
Downloaded 13729792 of 34212021 bytes (40.1%,    4.5s remaining)
Downloaded 18178048 of 34212021 bytes (53.1%,    3.6s remaining)
Downloaded 22790144 of 34212021 bytes (66.6%,    2.5s remaining)
Downloaded 27705344 of 34212021 bytes (81.0%,    1.4s remaining)
Downloaded 32694272 of 34212021 bytes (95.6%,    0.3s remaining) ...done. (8 seconds, 0 min)
Extracting data from /github/home/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2025-01-27 11:18:06,924 - JUNIFER - INFO - Reading BOLD from /tmp/tmpolnbfw8b/sub001_bold.nii.gz
2025-01-27 11:18:06,924 - JUNIFER - INFO - BOLD is of type NIFTI
2025-01-27 11:18:06,925 - JUNIFER - INFO - Reading T1w from /tmp/tmpolnbfw8b/sub001_T1w.nii.gz
2025-01-27 11:18:06,925 - JUNIFER - INFO - T1w is of type NIFTI
2025-01-27 11:18:06,925 - JUNIFER - INFO - Computing BOLD
2025-01-27 11:18:06,925 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-01-27 11:18:06,926 - JUNIFER - INFO - Parcellation parameters:
2025-01-27 11:18:06,926 - JUNIFER - INFO -      resolution: None
2025-01-27 11:18:06,926 - JUNIFER - INFO -      n_rois: 100
2025-01-27 11:18:06,926 - JUNIFER - INFO -      yeo_networks: 7
2025-01-27 11:18:06,926 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-01-27 11:18:08,176 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v1.0.0/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2025-01-27 11:18:10,093 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-01-27 11:18:10,593 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_62ea0ecc-dca0-11ef-bd11-0242ac120002r3dfl9ya/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_62ea0ecc-dca0-11ef-bd11-0242ac120002r3dfl9ya/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v1.0.0/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpfl6tpiz7/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_62ea0ecc-dca0-11ef-bd11-0242ac120002r3dfl9ya/parcellation_warped.nii.gz
2025-01-27 11:18:16,822 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2025-01-27 11:18:19,588 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)