diff --git a/doc/whats_new.rst b/doc/whats_new.rst index eed06930d0..b341c8cdb2 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -66,6 +66,9 @@ Fixes - :func:`nilearn.plotting.plot_matrix` providing labels=None, False, or an empty list now correctly disables labels. - :func:`nilearn.datasets.fetch_surf_nki_enhanced` is now downloading the correct left and right functional surface data for each subject +- :func:`nilearn.datasets.fetch_atlas_schaefer_2018` now downloads from release + version 0.14.3 (instead of 0.8.1) by default, which includes corrected region label + names along with 700 and 900 region parcelations. - Colormap creation functions have been updated to avoid matplotlib deprecation warnings about colormap reversal diff --git a/nilearn/datasets/atlas.py b/nilearn/datasets/atlas.py index 2be84139d8..3897f95110 100644 --- a/nilearn/datasets/atlas.py +++ b/nilearn/datasets/atlas.py @@ -1275,7 +1275,7 @@ def fetch_atlas_schaefer_2018(n_rois=400, yeo_networks=7, resolution_mm=1, ---------- n_rois: int number of regions of interest {100, 200, 300, 400 (default), 500, 600, - 800, 1000} + 700, 800, 900, 1000} yeo_networks: int ROI annotation according to yeo networks {7 (default), 17} @@ -1307,7 +1307,7 @@ def fetch_atlas_schaefer_2018(n_rois=400, yeo_networks=7, resolution_mm=1, References ---------- For more information on this dataset, see - https://github.com/ThomasYeoLab/CBIG/tree/v0.8.1-Schaefer2018_LocalGlobal/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal + https://github.com/ThomasYeoLab/CBIG/tree/v0.14.3-Update_Yeo2011_Schaefer2018_labelname/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations Schaefer A, Kong R, Gordon EM, Laumann TO, Zuo XN, Holmes AJ, Eickhoff SB, Yeo BTT. Local-Global parcellation of the human @@ -1320,8 +1320,15 @@ def fetch_atlas_schaefer_2018(n_rois=400, yeo_networks=7, resolution_mm=1, intrinsic functional connectivity. J Neurophysiol 106(3):1125-65, 2011. Licence: MIT. + + Notes + ----- + Release v0.14.3 of the Schaefer 2018 parcellation is used by + default. Versions prior to v0.14.3 are known to contain erroneous region + label names. For more details, see + https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/Updates/Update_20190916_README.md """ - valid_n_rois = [100, 200, 300, 400, 500, 600, 800, 1000] + valid_n_rois = list(range(100, 1100, 100)) valid_yeo_networks = [7, 17] valid_resolution_mm = [1, 2] if n_rois not in valid_n_rois: @@ -1338,9 +1345,9 @@ def fetch_atlas_schaefer_2018(n_rois=400, yeo_networks=7, resolution_mm=1, if base_url is None: base_url = ('https://raw.githubusercontent.com/ThomasYeoLab/CBIG/' - 'v0.8.1-Schaefer2018_LocalGlobal/stable_projects/' - 'brain_parcellation/Schaefer2018_LocalGlobal/' - 'Parcellations/MNI/' + 'v0.14.3-Update_Yeo2011_Schaefer2018_labelname/' + 'stable_projects/brain_parcellation/' + 'Schaefer2018_LocalGlobal/Parcellations/MNI/' ) files = [] diff --git a/nilearn/datasets/tests/test_atlas.py b/nilearn/datasets/tests/test_atlas.py index e6984c4d6c..a2ce5b8cf1 100644 --- a/nilearn/datasets/tests/test_atlas.py +++ b/nilearn/datasets/tests/test_atlas.py @@ -565,7 +565,7 @@ def test_fetch_atlas_pauli_2017(): @with_setup(tst.setup_tmpdata, tst.teardown_tmpdata) def test_fetch_atlas_schaefer_2018(): - valid_n_rois = [100, 200, 300, 400, 500, 600, 800, 1000] + valid_n_rois = list(range(100, 1100, 100)) valid_yeo_networks = [7, 17] valid_resolution_mm = [1, 2]