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:139: 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))
2024-11-13 15:30:34,980 - JUNIFER - INFO - ===== Lib Versions =====
2024-11-13 15:30:34,980 - JUNIFER - INFO - numpy: 1.26.4
2024-11-13 15:30:34,980 - JUNIFER - INFO - scipy: 1.14.1
2024-11-13 15:30:34,980 - JUNIFER - INFO - pandas: 2.1.4
2024-11-13 15:30:34,980 - JUNIFER - INFO - nilearn: 0.10.4
2024-11-13 15:30:34,980 - JUNIFER - INFO - nibabel: 5.3.2
2024-11-13 15:30:34,980 - JUNIFER - INFO - junifer: 0.0.6.dev252
2024-11-13 15:30:34,980 - 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)

2024-11-13 15:30:34,986 - JUNIFER - INFO - Getting element sub-01
2024-11-13 15:30:34,986 - JUNIFER - INFO - Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-11-13 15:30:34,986 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-11-13 15:30:34,987 - JUNIFER - INFO - Computing VBM_GM
2024-11-13 15:30:34,987 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-11-13 15:30:34,987 - JUNIFER - INFO - Parcellation parameters:
2024-11-13 15:30:34,988 - JUNIFER - INFO -      resolution: 2.0
2024-11-13 15:30:34,988 - JUNIFER - INFO -      n_rois: 100
2024-11-13 15:30:34,988 - JUNIFER - INFO -      yeo_networks: 7
2024-11-13 15:30:34,988 - 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_2mm.nii.gz ...
 ...done. (0 seconds, 0 min)
2024-11-13 15:30:35,133 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-11-13 15:30:35,188 - 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
2024-11-13 15:30:36,357 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-11-13 15:30:36,437 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3a18bbb2-a1d4-11ef-a09a-0242ac120002zgtoyg20/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3a18bbb2-a1d4-11ef-a09a-0242ac120002zgtoyg20/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/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3a18bbb2-a1d4-11ef-a09a-0242ac120002zgtoyg20/parcellation_warped.nii.gz
2024-11-13 15:30:38,228 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-11-13 15:30:39,433 - 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)

2024-11-13 15:30:39,434 - 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 1277952 of 34212021 bytes (3.7%,   26.5s remaining)
Downloaded 6250496 of 34212021 bytes (18.3%,    9.2s remaining)
Downloaded 10166272 of 34212021 bytes (29.7%,    7.3s remaining)
Downloaded 12648448 of 34212021 bytes (37.0%,    7.0s remaining)
Downloaded 15335424 of 34212021 bytes (44.8%,    6.3s remaining)
Downloaded 18112512 of 34212021 bytes (52.9%,    5.5s remaining)
Downloaded 20955136 of 34212021 bytes (61.3%,    4.5s remaining)
Downloaded 23814144 of 34212021 bytes (69.6%,    3.6s remaining)
Downloaded 26664960 of 34212021 bytes (77.9%,    2.6s remaining)
Downloaded 29532160 of 34212021 bytes (86.3%,    1.6s remaining)
Downloaded 32432128 of 34212021 bytes (94.8%,    0.6s remaining) ...done. (13 seconds, 0 min)
Extracting data from /github/home/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2024-11-13 15:30:55,089 - JUNIFER - INFO - Reading BOLD from /tmp/tmp6cv8gx6w/sub001_bold.nii.gz
2024-11-13 15:30:55,089 - JUNIFER - INFO - BOLD is of type NIFTI
2024-11-13 15:30:55,090 - JUNIFER - INFO - Reading T1w from /tmp/tmp6cv8gx6w/sub001_T1w.nii.gz
2024-11-13 15:30:55,090 - JUNIFER - INFO - T1w is of type NIFTI
2024-11-13 15:30:55,091 - JUNIFER - INFO - Computing BOLD
2024-11-13 15:30:55,091 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-11-13 15:30:55,092 - JUNIFER - INFO - Parcellation parameters:
2024-11-13 15:30:55,092 - JUNIFER - INFO -      resolution: 3.0
2024-11-13 15:30:55,092 - JUNIFER - INFO -      n_rois: 100
2024-11-13 15:30:55,092 - JUNIFER - INFO -      yeo_networks: 7
2024-11-13 15:30:55,093 - JUNIFER - INFO - Loading parcellation: /github/home/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-11-13 15:30:55,147 - 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
2024-11-13 15:30:56,280 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-11-13 15:30:56,360 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/junifer/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_45fe4b18-a1d4-11ef-a09a-0242ac120002q2dkzwhc/prewarp_parcellation.nii.gz -r /tmp/junifer/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_45fe4b18-a1d4-11ef-a09a-0242ac120002q2dkzwhc/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/tmp_u91_mvv/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_45fe4b18-a1d4-11ef-a09a-0242ac120002q2dkzwhc/parcellation_warped.nii.gz
2024-11-13 15:30:58,155 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-11-13 15:31:00,838 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)

Total running time of the script: (0 minutes 25.864 seconds)

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