.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/run_compute_parcel_mean.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_run_compute_parcel_mean.py: 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 .. GENERATED FROM PYTHON SOURCE LINES 13-25 .. code-block:: Python from junifer.testing.datagrabbers import ( OasisVBMTestingDataGrabber, SPMAuditoryTestingDataGrabber, ) from junifer.datagrabber import DataType from junifer.datareader import DefaultDataReader from junifer.markers import ParcelAggregation from junifer.stats import AggFunc from junifer.utils import configure_logging .. GENERATED FROM PYTHON SOURCE LINES 26-27 Set the logging level to info to see extra information .. GENERATED FROM PYTHON SOURCE LINES 27-29 .. code-block:: Python configure_logging(level="INFO") .. rst-class:: sphx-glr-script-out .. code-block:: none 2025-11-18 17:37:04 [info ] ===== Lib Versions ===== [junifer] 2025-11-18 17:37:04 [info ] click: 8.1.8 [junifer] 2025-11-18 17:37:04 [info ] numpy: 1.26.4 [junifer] 2025-11-18 17:37:04 [info ] scipy: 1.15.0 [junifer] 2025-11-18 17:37:04 [info ] datalad: 1.1.6 [junifer] 2025-11-18 17:37:04 [info ] pandas: 2.1.4 [junifer] 2025-11-18 17:37:04 [info ] nibabel: 5.3.2 [junifer] 2025-11-18 17:37:04 [info ] nilearn: 0.10.4 [junifer] 2025-11-18 17:37:04 [info ] sqlalchemy: 2.0.44 [junifer] 2025-11-18 17:37:04 [info ] ruamel.yaml: 0.18.16 [junifer] 2025-11-18 17:37:04 [info ] tqdm: 4.66.6 [junifer] 2025-11-18 17:37:04 [info ] templateflow: 24.2.2 [junifer] 2025-11-18 17:37:04 [info ] junifer_data: None [junifer] 2025-11-18 17:37:04 [info ] junifer: 0.0.7.dev401 [junifer] 2025-11-18 17:37:04 [info ] ======================== [junifer] .. GENERATED FROM PYTHON SOURCE LINES 30-31 Perform parcel aggregation on VBM GM data (3D) from OASIS dataset .. GENERATED FROM PYTHON SOURCE LINES 31-47 .. code-block:: Python 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=AggFunc.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) .. rst-class:: sphx-glr-script-out .. code-block:: none 2025-11-18 17:37:04 [info ] Getting element ('sub-01',) [junifer] 2025-11-18 17:37:04 [info ] Reading VBM_GM from /github/home/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz [junifer] 2025-11-18 17:37:04 [info ] VBM_GM is of type NIFTI [junifer] 2025-11-18 17:37:04 [info ] Computing DataType.VBM_GM [junifer] 2025-11-18 17:37:04 [info ] Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution [junifer] 2025-11-18 17:37:04 [info ] Parcellation parameters: [junifer] 2025-11-18 17:37:04 [info ] resolution: None [junifer] 2025-11-18 17:37:04 [info ] n_rois: 100 [junifer] 2025-11-18 17:37:04 [info ] yeo_networks: 7 [junifer] 2025-11-18 17:37:04 [info ] Resolution set to None, using highest resolution. [junifer] 2025-11-18 17:37:04 [info ] Start annex operation [datalad.annex] dlm_progress=annexprogress-139689200586000 dlm_progress_label=Total dlm_progress_noninteractive_level=5 dlm_progress_total=233605 dlm_progress_unit=' Bytes' 2025-11-18 17:37:05 [info ] Start annex action: {'command': 'get', 'file': 'parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz', 'input': ['parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz'], 'key': 'MD5E-s233605--0709e73f84a0cd60687ff4add7f8fd05.nii.gz', 'note': 'from gin-src...'} [datalad.annex] dlm_progress=annexprogress-139689200586000-5135629851891593778 dlm_progress_label='Get parcella .. 2_1mm.nii.gz' dlm_progress_noninteractive_level=5 dlm_progress_total=233605.0 dlm_progress_unit=' Bytes' 2025-11-18 17:37:05 [info ] 14.03% [datalad.annex] dlm_progress=annexprogress-139689200586000-5135629851891593778 dlm_progress_noninteractive_level=5 dlm_progress_update=32768.0 2025-11-18 17:37:06 [info ] 63.12% [datalad.annex] dlm_progress=annexprogress-139689200586000-5135629851891593778 dlm_progress_noninteractive_level=5 dlm_progress_update=147456.0 2025-11-18 17:37:06 [info ] Finished annex action: None [datalad.annex] dlm_progress=annexprogress-139689200586000-5135629851891593778 dlm_progress_noninteractive_level=5 2025-11-18 17:37:06 [info ] Finished annex get [datalad.annex] dlm_progress=annexprogress-139689200586000 dlm_progress_noninteractive_level=5 2025-11-18 17:37:06 [info ] Loading parcellation: /github/home/junifer_data/v5/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz [junifer] 2025-11-18 17:37:08 [info ] Downloading template MNI152Lin (T1w in resolution 1) [junifer] 2025-11-18 17:37:09 [info ] antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_33da1a4e-c4a5-11f0-a26b-be2f509f929d_80esxv9/prewarp_parcellation.nii.gz -r /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_33da1a4e-c4a5-11f0-a26b-be2f509f929d_80esxv9/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v5/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_33da1a4e-c4a5-11f0-a26b-be2f509f929d_80esxv9/parcellation_warped.nii.gz [junifer] 2025-11-18 17:37:15 [info ] antsApplyTransforms command succeeded with the following output: [junifer] 2025-11-18 17:37:17 [info ] No storage specified, returning dictionary [junifer] dict_keys([]) (1, 100) .. GENERATED FROM PYTHON SOURCE LINES 48-49 Perform parcel aggregation on BOLD data (4D) from SPM Auditory dataset .. GENERATED FROM PYTHON SOURCE LINES 49-65 .. code-block:: Python 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=AggFunc.Mean, on=[DataType.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) .. rst-class:: sphx-glr-script-out .. code-block:: none 2025-11-18 17:37:17 [info ] Getting element ('sub001',) [junifer] 2025-11-18 17:37:19 [info ] Reading BOLD from /tmp/tmpf7c8v3r_/sub001_bold.nii.gz [junifer] 2025-11-18 17:37:19 [info ] BOLD is of type NIFTI [junifer] 2025-11-18 17:37:19 [info ] Reading T1w from /tmp/tmpf7c8v3r_/sub001_T1w.nii.gz [junifer] 2025-11-18 17:37:19 [info ] T1w is of type NIFTI [junifer] 2025-11-18 17:37:19 [info ] Computing DataType.BOLD [junifer] 2025-11-18 17:37:19 [info ] Parcellation will be warped from MNI152NLin6Asym to MNI152Lin using highest resolution [junifer] 2025-11-18 17:37:19 [info ] Parcellation parameters: [junifer] 2025-11-18 17:37:19 [info ] resolution: None [junifer] 2025-11-18 17:37:19 [info ] n_rois: 100 [junifer] 2025-11-18 17:37:19 [info ] yeo_networks: 7 [junifer] 2025-11-18 17:37:19 [info ] Resolution set to None, using highest resolution. [junifer] 2025-11-18 17:37:19 [info ] Loading parcellation: /github/home/junifer_data/v5/parcellations/Schaefer2018/Yeo2011/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii.gz [junifer] 2025-11-18 17:37:21 [info ] Downloading template MNI152Lin (T1w in resolution 1) [junifer] 2025-11-18 17:37:22 [info ] antsApplyTransforms command to be executed: antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3b71d224-c4a5-11f0-a26b-be2f509f929d8zvtpnyc/prewarp_parcellation.nii.gz -r /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3b71d224-c4a5-11f0-a26b-be2f509f929d8zvtpnyc/MNI152Lin_T1w.nii.gz -t /github/home/junifer_data/v5/.git/annex/objects/JQ/Pp/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5/SHA256E-s145422752--5091350b36f951d455dabd429ebe86c493c75a0217dca311ae355f1d62e080b0.h5 -o /tmp/tmpuuq7ljtr/ants_parcellation_warper_Schaefer100x7_from_MNI152NLin6Asym_to_MNI152Lin_3b71d224-c4a5-11f0-a26b-be2f509f929d8zvtpnyc/parcellation_warped.nii.gz [junifer] 2025-11-18 17:37:28 [info ] antsApplyTransforms command succeeded with the following output: [junifer] 2025-11-18 17:37:31 [info ] No storage specified, returning dictionary [junifer] dict_keys([]) (96, 100) .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 27.054 seconds) .. _sphx_glr_download_auto_examples_run_compute_parcel_mean.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: run_compute_parcel_mean.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: run_compute_parcel_mean.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: run_compute_parcel_mean.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_