Note

Go to the end to download the full example code.

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))
2024-12-09 11:21:18,037 - JUNIFER - INFO - ===== Lib Versions =====
2024-12-09 11:21:18,037 - JUNIFER - INFO - numpy: 1.26.4
2024-12-09 11:21:18,037 - JUNIFER - INFO - scipy: 1.14.1
2024-12-09 11:21:18,037 - JUNIFER - INFO - pandas: 2.1.4
2024-12-09 11:21:18,037 - JUNIFER - INFO - nilearn: 0.10.4
2024-12-09 11:21:18,037 - JUNIFER - INFO - nibabel: 5.3.2
2024-12-09 11:21:18,037 - JUNIFER - INFO - junifer: 0.0.6.dev366
2024-12-09 11:21:18,037 - 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)

2024-12-09 11:21:18,043 - JUNIFER - INFO - Getting element sub-01
2024-12-09 11:21:18,043 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-12-09 11:21:18,043 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-12-09 11:21:18,044 - JUNIFER - INFO - Computing VBM_GM
2024-12-09 11:21:18,044 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:21:18,044 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:21:18,044 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:21:18,044 - JUNIFER - INFO -      resolution: None
2024-12-09 11:21:18,044 - JUNIFER - INFO -      n_rois: 100
2024-12-09 11:21:18,044 - JUNIFER - INFO -      yeo_networks: 7
2024-12-09 11:21:18,044 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:21:18,045 - 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)
2024-12-09 11:21:18,610 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:21:18,882 - 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
2024-12-09 11:21:19,969 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:21:20,473 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b62f2448-b61f-11ef-88f6-0242ac120002u9m96_4v/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b62f2448-b61f-11ef-88f6-0242ac120002u9m96_4v/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/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_b62f2448-b61f-11ef-88f6-0242ac120002u9m96_4v/parcellation_warped.nii.gz
2024-12-09 11:21:29,506 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-12-09 11:21:30,872 - 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)

2024-12-09 11:21:30,873 - 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 1122304 of 34212021 bytes (3.3%,   29.9s remaining)
Downloaded 5251072 of 34212021 bytes (15.3%,   11.1s remaining)
Downloaded 8175616 of 34212021 bytes (23.9%,    9.6s remaining)
Downloaded 11059200 of 34212021 bytes (32.3%,    8.4s remaining)
Downloaded 13426688 of 34212021 bytes (39.2%,    7.8s remaining)
Downloaded 15966208 of 34212021 bytes (46.7%,    6.9s remaining)
Downloaded 18595840 of 34212021 bytes (54.4%,    5.9s remaining)
Downloaded 21274624 of 34212021 bytes (62.2%,    4.9s remaining)
Downloaded 23961600 of 34212021 bytes (70.0%,    3.9s remaining)
Downloaded 26648576 of 34212021 bytes (77.9%,    2.9s remaining)
Downloaded 29351936 of 34212021 bytes (85.8%,    1.8s remaining)
Downloaded 32079872 of 34212021 bytes (93.8%,    0.8s remaining) ...done. (15 seconds, 0 min)
Extracting data from /github/home/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2024-12-09 11:21:48,540 - JUNIFER - INFO - Reading BOLD from /tmp/tmpc3m3pyan/sub001_bold.nii.gz
2024-12-09 11:21:48,540 - JUNIFER - INFO - BOLD is of type NIFTI
2024-12-09 11:21:48,541 - JUNIFER - INFO - Reading T1w from /tmp/tmpc3m3pyan/sub001_T1w.nii.gz
2024-12-09 11:21:48,541 - JUNIFER - INFO - T1w is of type NIFTI
2024-12-09 11:21:48,542 - JUNIFER - INFO - Computing BOLD
2024-12-09 11:21:48,542 - JUNIFER - INFO - Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution
2024-12-09 11:21:48,543 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-12-09 11:21:48,543 - JUNIFER - INFO - Parcellation parameters:
2024-12-09 11:21:48,543 - JUNIFER - INFO -      resolution: None
2024-12-09 11:21:48,543 - JUNIFER - INFO -      n_rois: 100
2024-12-09 11:21:48,543 - JUNIFER - INFO -      yeo_networks: 7
2024-12-09 11:21:48,543 - JUNIFER - INFO - Resolution set to None, using highest resolution.
2024-12-09 11:21:48,544 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz
2024-12-09 11:21:48,813 - 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
2024-12-09 11:21:49,896 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 1
2024-12-09 11:21:50,398 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_c8065aec-b61f-11ef-88f6-0242ac120002jpm2miyk/prewarp_parcellation.nii.gz -r /tmp/junifer/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_c8065aec-b61f-11ef-88f6-0242ac120002jpm2miyk/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/tmpmvdfxj1i/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_c8065aec-b61f-11ef-88f6-0242ac120002jpm2miyk/parcellation_warped.nii.gz
2024-12-09 11:21:59,387 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-12-09 11:22:02,336 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)

Total running time of the script: (0 minutes 44.304 seconds)

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