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))
2024-12-06 13:54:33,189 - JUNIFER - INFO - ===== Lib Versions =====
2024-12-06 13:54:33,189 - JUNIFER - INFO - numpy: 1.26.4
2024-12-06 13:54:33,189 - JUNIFER - INFO - scipy: 1.14.1
2024-12-06 13:54:33,189 - JUNIFER - INFO - pandas: 2.1.4
2024-12-06 13:54:33,189 - JUNIFER - INFO - nilearn: 0.10.4
2024-12-06 13:54:33,189 - JUNIFER - INFO - nibabel: 5.3.2
2024-12-06 13:54:33,190 - JUNIFER - INFO - junifer: 0.0.6.dev358
2024-12-06 13:54:33,190 - 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)

2024-12-06 13:54:33,195 - JUNIFER - INFO - Getting element sub-01
2024-12-06 13:54:33,196 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-06 13:54:33,196 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-06 13:54:33,197 - JUNIFER - INFO - Computing VBM_GM
2024-12-06 13:54:33,197 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:54:33,197 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:54:33,197 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:54:33,197 - JUNIFER - INFO -      resolution: None
2024-12-06 13:54:33,197 - JUNIFER - INFO -      n_rois: 100
2024-12-06 13:54:33,197 - JUNIFER - INFO -      yeo_networks: 7
2024-12-06 13:54:33,197 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:54:33,197 - JUNIFER - INFO - At least one of the parcellation files are missing. Fetching using nilearn.
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_100Parcels_7Networks_order.txt ...
 ...done. (0 seconds, 0 min)
Downloading data from https://raw.githubusercontent.com/ThomasYeoLab/CBIG/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/MNI/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz ...
 ...done. (0 seconds, 0 min)
2024-12-06 13:54:33,602 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:54:33,870 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:54:34,985 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:54:35,488 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_9f95af6a-b3d9-11ef-9645-0242ac1200022dss0j1g/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_9f95af6a-b3d9-11ef-9645-0242ac1200022dss0j1g/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_9f95af6a-b3d9-11ef-9645-0242ac1200022dss0j1g/parcellation_warped.nii.gz
2024-12-06 13:54:44,568 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-12-06 13:54:45,864 - 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)

2024-12-06 13:54:45,865 - 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 1499136 of 34212021 bytes (4.4%,   22.2s remaining)
Downloaded 6324224 of 34212021 bytes (18.5%,    9.1s remaining)
Downloaded 13352960 of 34212021 bytes (39.0%,    4.8s remaining)
Downloaded 18505728 of 34212021 bytes (54.1%,    3.5s remaining)
Downloaded 20856832 of 34212021 bytes (61.0%,    3.3s remaining)
Downloaded 22880256 of 34212021 bytes (66.9%,    3.0s remaining)
Downloaded 25026560 of 34212021 bytes (73.2%,    2.6s remaining)
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Downloaded 31645696 of 34212021 bytes (92.5%,    0.8s remaining)
Downloaded 33857536 of 34212021 bytes (99.0%,    0.1s remaining) ...done. (13 seconds, 0 min)
Extracting data from /github/home/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2024-12-06 13:55:01,408 - JUNIFER - INFO - Reading BOLD from /tmp/tmpwfx19g14/sub001_bold.nii.gz
2024-12-06 13:55:01,408 - JUNIFER - INFO - BOLD is of type NIFTI
2024-12-06 13:55:01,409 - JUNIFER - INFO - Reading T1w from /tmp/tmpwfx19g14/sub001_T1w.nii.gz
2024-12-06 13:55:01,409 - JUNIFER - INFO - T1w is of type NIFTI
2024-12-06 13:55:01,410 - JUNIFER - INFO - Computing BOLD
2024-12-06 13:55:01,410 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-06 13:55:01,410 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-06 13:55:01,410 - JUNIFER - INFO - Parcellation parameters:
2024-12-06 13:55:01,410 - JUNIFER - INFO -      resolution: None
2024-12-06 13:55:01,410 - JUNIFER - INFO -      n_rois: 100
2024-12-06 13:55:01,410 - JUNIFER - INFO -      yeo_networks: 7
2024-12-06 13:55:01,410 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-06 13:55:01,412 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2024-12-06 13:55:01,682 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5
2024-12-06 13:55:02,799 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-06 13:55:03,304 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b02969ca-b3d9-11ef-9645-0242ac120002efcxyjrw/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b02969ca-b3d9-11ef-9645-0242ac120002efcxyjrw/MNI152Lin_T1w.nii.gz -t /github/home/junifer/data/xfms/.git/annex/objects/80/1W/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5/SHA256E-s151956315--b80fd5f087580ecbbb212d1ece24c12f1ce448ca4912c1ea739eb8e84b6f418a.h5 -o /tmp/junifer/tmp28sxvvtd/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b02969ca-b3d9-11ef-9645-0242ac120002efcxyjrw/parcellation_warped.nii.gz
2024-12-06 13:55:12,330 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

/__t/Python/3.12.7/x64/lib/python3.12/site-packages/nilearn/maskers/nifti_masker.py:110: UserWarning: imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.
  warnings.warn(
2024-12-06 13:55:14,686 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)