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:155: 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))
2025-05-09 12:39:24,958 - JUNIFER - INFO - ===== Lib Versions =====
2025-05-09 12:39:24,958 - JUNIFER - INFO - click: 8.1.8
2025-05-09 12:39:24,958 - JUNIFER - INFO - numpy: 1.26.4
2025-05-09 12:39:24,958 - JUNIFER - INFO - scipy: 1.15.0
2025-05-09 12:39:24,958 - JUNIFER - INFO - datalad: 1.1.5
2025-05-09 12:39:24,958 - JUNIFER - INFO - pandas: 2.1.4
2025-05-09 12:39:24,958 - JUNIFER - INFO - nibabel: 5.3.2
2025-05-09 12:39:24,958 - JUNIFER - INFO - nilearn: 0.10.4
2025-05-09 12:39:24,958 - JUNIFER - INFO - sqlalchemy: 2.0.40
2025-05-09 12:39:24,959 - JUNIFER - INFO - ruamel.yaml: 0.18.10
2025-05-09 12:39:24,959 - JUNIFER - INFO - tqdm: 4.66.6
2025-05-09 12:39:24,959 - JUNIFER - INFO - templateflow: 24.2.2
2025-05-09 12:39:24,959 - JUNIFER - INFO - junifer_data: None
2025-05-09 12:39:24,959 - JUNIFER - INFO - junifer: 0.0.7.dev83
2025-05-09 12:39:24,959 - 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)

2025-05-09 12:39:24,964 - JUNIFER - INFO - Getting element sub-01
2025-05-09 12:39:24,965 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2025-05-09 12:39:24,965 - JUNIFER - INFO - VBM_GM is of type NIFTI
2025-05-09 12:39:24,966 - JUNIFER - INFO - Computing VBM_GM
2025-05-09 12:39:24,966 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:39:24,966 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:39:24,966 - JUNIFER - INFO -      resolution: None
2025-05-09 12:39:24,966 - JUNIFER - INFO -      n_rois: 100
2025-05-09 12:39:24,966 - JUNIFER - INFO -      yeo_networks: 7
2025-05-09 12:39:24,966 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:39:25,040 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:39:27,334 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:39:27,840 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_a3e40428-2cd2-11f0-b407-763dc8eb2af0bhd7b19r/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_a3e40428-2cd2-11f0-b407-763dc8eb2af0bhd7b19r/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_a3e40428-2cd2-11f0-b407-763dc8eb2af0bhd7b19r/parcellation_warped.nii.gz
2025-05-09 12:39:34,072 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2025-05-09 12:39:35,397 - 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)

2025-05-09 12:39:35,398 - 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 1310720 of 34212021 bytes (3.8%,   25.9s remaining)
Downloaded 6447104 of 34212021 bytes (18.8%,    8.8s remaining)
Downloaded 11329536 of 34212021 bytes (33.1%,    6.2s remaining)
Downloaded 16490496 of 34212021 bytes (48.2%,    4.4s remaining)
Downloaded 21209088 of 34212021 bytes (62.0%,    3.1s remaining)
Downloaded 24002560 of 34212021 bytes (70.2%,    2.6s remaining)
Downloaded 27017216 of 34212021 bytes (79.0%,    1.9s remaining)
Downloaded 30162944 of 34212021 bytes (88.2%,    1.1s remaining)
Downloaded 33374208 of 34212021 bytes (97.6%,    0.2s remaining) ...done. (11 seconds, 0 min)
Extracting data from /github/home/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2025-05-09 12:39:48,989 - JUNIFER - INFO - Reading BOLD from /tmp/tmpv0_2dc8x/sub001_bold.nii.gz
2025-05-09 12:39:48,989 - JUNIFER - INFO - BOLD is of type NIFTI
2025-05-09 12:39:48,990 - JUNIFER - INFO - Reading T1w from /tmp/tmpv0_2dc8x/sub001_T1w.nii.gz
2025-05-09 12:39:48,990 - JUNIFER - INFO - T1w is of type NIFTI
2025-05-09 12:39:48,991 - JUNIFER - INFO - Computing BOLD
2025-05-09 12:39:48,991 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2025-05-09 12:39:48,991 - JUNIFER - INFO - Parcellation parameters:
2025-05-09 12:39:48,991 - JUNIFER - INFO -      resolution: None
2025-05-09 12:39:48,991 - JUNIFER - INFO -      n_rois: 100
2025-05-09 12:39:48,991 - JUNIFER - INFO -      yeo_networks: 7
2025-05-09 12:39:48,991 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2025-05-09 12:39:49,065 - JUNIFER - INFO - Loading parcellation: /github/home/junifer_data/v2/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2025-05-09 12:39:51,338 - JUNIFER - INFO - Downloading template MNI152Lin (T1w in resolution 1)
2025-05-09 12:39:51,842 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b235b044-2cd2-11f0-b407-763dc8eb2af0nxbbrjem/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b235b044-2cd2-11f0-b407-763dc8eb2af0nxbbrjem/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v2/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/junifer/tmpxe1wwcwb/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b235b044-2cd2-11f0-b407-763dc8eb2af0nxbbrjem/parcellation_warped.nii.gz
2025-05-09 12:39:58,134 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2025-05-09 12:40:01,105 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)