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")

2024-09-30 11:46:58,539 - JUNIFER - INFO - ===== Lib Versions =====
2024-09-30 11:46:58,539 - JUNIFER - INFO - numpy: 1.26.4
2024-09-30 11:46:58,540 - JUNIFER - INFO - scipy: 1.14.0
2024-09-30 11:46:58,540 - JUNIFER - INFO - pandas: 2.1.4
2024-09-30 11:46:58,540 - JUNIFER - INFO - nilearn: 0.10.4
2024-09-30 11:46:58,540 - JUNIFER - INFO - nibabel: 5.2.1
2024-09-30 11:46:58,540 - JUNIFER - INFO - junifer: 0.0.6.dev90
2024-09-30 11:46:58,540 - 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)

2024-09-30 11:46:58,545 - JUNIFER - INFO - Getting element sub-01
2024-09-30 11:46:58,545 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-09-30 11:46:58,545 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-09-30 11:46:58,546 - JUNIFER - INFO - Computing VBM_GM
2024-09-30 11:46:58,547 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:46:58,547 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:46:58,547 - JUNIFER - INFO -      resolution: 2.0
2024-09-30 11:46:58,547 - JUNIFER - INFO -      n_rois: 100
2024-09-30 11:46:58,547 - JUNIFER - INFO -      yeo_networks: 7
2024-09-30 11:46:58,547 - 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)
2024-09-30 11:46:58,588 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:46:58,617 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:46:59,600 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:46:59,697 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellationsxdkcoc6n/Schaefer100x7.nii.gz -r /tmp/tmpn9vwo4yf/parcellationsxdkcoc6n/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp16ha0i5x/parcellationsm27teqqc/Schaefer100x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:01,089 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-09-30 11:47:02,025 - 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)

2024-09-30 11:47:02,026 - JUNIFER - INFO - Getting element sub001

Dataset created in /home/runner/nilearn_data/spm_auditory

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

Downloaded 4456448 of 34212021 bytes (13.0%,    6.9s remaining)
Downloaded 11681792 of 34212021 bytes (34.1%,    3.9s remaining)
Downloaded 16596992 of 34212021 bytes (48.5%,    3.2s remaining)
Downloaded 20652032 of 34212021 bytes (60.4%,    2.7s remaining)
Downloaded 25092096 of 34212021 bytes (73.3%,    1.8s remaining)
Downloaded 29474816 of 34212021 bytes (86.2%,    1.0s remaining)
Downloaded 34144256 of 34212021 bytes (99.8%,    0.0s remaining) ...done. (8 seconds, 0 min)
Extracting data from /home/runner/nilearn_data/spm_auditory/sub001/MoAEpilot.zip..... done.
2024-09-30 11:47:13,522 - JUNIFER - INFO - Reading BOLD from /tmp/tmppjz_i635/sub001_bold.nii.gz
2024-09-30 11:47:13,523 - JUNIFER - INFO - BOLD is of type NIFTI
2024-09-30 11:47:13,523 - JUNIFER - INFO - Reading T1w from /tmp/tmppjz_i635/sub001_T1w.nii.gz
2024-09-30 11:47:13,524 - JUNIFER - INFO - T1w is of type NIFTI
2024-09-30 11:47:13,524 - JUNIFER - INFO - Computing BOLD
2024-09-30 11:47:13,525 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-09-30 11:47:13,525 - JUNIFER - INFO - Parcellation parameters:
2024-09-30 11:47:13,525 - JUNIFER - INFO -      resolution: 3.0
2024-09-30 11:47:13,525 - JUNIFER - INFO -      n_rois: 100
2024-09-30 11:47:13,525 - JUNIFER - INFO -      yeo_networks: 7
2024-09-30 11:47:13,527 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_2mm.nii.gz
2024-09-30 11:47:13,557 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-09-30 11:47:14,552 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-09-30 11:47:14,649 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpn9vwo4yf/parcellations37_nytpz/Schaefer100x7.nii.gz -r /tmp/tmpn9vwo4yf/parcellations37_nytpz/MNI152Lin_T1w_3.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp16ha0i5x/parcellations42jaau08/Schaefer100x7_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-09-30 11:47:16,032 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:

2024-09-30 11:47:18,689 - JUNIFER - INFO - No storage specified, returning dictionary
dict_keys(['BOLD'])
(96, 100)