MRG, ENH: Add infant template downloader (mne-tools#8738)

* ENH: Add infant template downloader * TST: Add test * Update tutorials/source-modeling/plot_eeg_no_mri.py Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Daniel McCloy <[email protected]>
rmc-law · Jan 20, 2021 · 5f17b35 · 5f17b35
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diff --git a/MANIFEST.in b/MANIFEST.in
@@ -19,6 +19,7 @@ recursive-include mne/data/image *
 recursive-include mne/data/fsaverage *
 include mne/datasets/_fsaverage/root.txt
 include mne/datasets/_fsaverage/bem.txt
+include mne/datasets/_infant/*.txt
 
 recursive-include mne/channels/data/layouts *
 recursive-include mne/channels/data/montages *

diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc
@@ -24,6 +24,8 @@ Enhancements
 
 - Add toggle-all button to :class:`mne.Report` HTML and ``width`` argument to :meth:`mne.Report.add_bem_to_section` (:gh:`8723` by `Eric Larson`_)
 
+- Add infant template MRI dataset downloader :func:`mne.datasets.fetch_infant_template` (:gh:`8738` by `Eric Larson`_ and `Christian O'Reilly`_)
+
 - Speed up :func:`mne.inverse_sparse.tf_mixed_norm` using STFT/ISTFT linearity (:gh:`8697` by `Eric Larson`_)
 
 - `mne.Report.parse_folder` now processes supported non-FIFF files by default, too (:gh:`8744` by `Richard Höchenberger`_)

diff --git a/doc/overview/datasets_index.rst b/doc/overview/datasets_index.rst
@@ -351,6 +351,12 @@ For convenience, we provide a function to separately download and extract the
 
     :ref:`tut-eeg-fsaverage-source-modeling`
 
+Infant template MRIs
+^^^^^^^^^^^^^^^^^^^^
+:func:`mne.datasets.fetch_infant_template`
+
+This function will download an infant template MRI from
+:footcite:`OReillyEtAl2021` along with MNE-specific files.
 
 ECoG Dataset
 ^^^^^^^^^^^^

diff --git a/doc/python_reference.rst b/doc/python_reference.rst
@@ -196,6 +196,7 @@ Datasets
    fetch_aparc_sub_parcellation
    fetch_fsaverage
    fetch_hcp_mmp_parcellation
+   fetch_infant_template
    fnirs_motor.data_path
    hf_sef.data_path
    kiloword.data_path

diff --git a/doc/references.bib b/doc/references.bib
@@ -1888,10 +1888,42 @@ @misc{WikipediaSI
     urldate = "12-October-2020"
 }
 
-
 @misc{BIDSdocs,
     author = "{BIDS} contributors",
     title = {Brain Imaging Data Structure — Specification},
     url = {https://bids-specification.readthedocs.io/en/stable/},
     urldate = "12-October-2020"
 }
+
+
+@article{OReillyEtAl2021,
+	title = {Structural templates for imaging {EEG} cortical sources in infants},
+	volume = {227},
+	issn = {1053-8119},
+	url = {http://www.sciencedirect.com/science/article/pii/S1053811920311678},
+	doi = {10.1016/j.neuroimage.2020.117682},
+	language = {en},
+	urldate = {2021-01-12},
+	journal = {NeuroImage},
+	author = {O'Reilly, Christian and Larson, Eric and Richards, John E. and Elsabbagh, Mayada},
+	month = feb,
+	year = {2021},
+	keywords = {Electroencephalography, Forward model, Infant, Neurodevelopment, Population template, Source reconstruction},
+	pages = {117682}
+}
+
+@article{RichardsEtAl2016,
+	series = {Sharing the wealth: {Brain} {Imaging} {Repositories} in 2015},
+	title = {A database of age-appropriate average {MRI} templates},
+	volume = {124},
+	issn = {1053-8119},
+	url = {http://www.sciencedirect.com/science/article/pii/S1053811915003559},
+	doi = {10.1016/j.neuroimage.2015.04.055},
+	language = {en},
+	journal = {NeuroImage},
+	author = {Richards, John E. and Sanchez, Carmen and Phillips-Meek, Michelle and Xie, Wanze},
+	month = jan,
+	year = {2016},
+	keywords = {Average MRI templates, Brain development, Lifespan MRI, Neurodevelopmental MRI Database},
+	pages = {1254--1259}
+}
diff --git a/mne/datasets/__init__.py b/mne/datasets/__init__.py
@@ -26,10 +26,11 @@
 from .utils import (_download_all_example_data, fetch_hcp_mmp_parcellation,
                     fetch_aparc_sub_parcellation)
 from ._fsaverage.base import fetch_fsaverage
+from ._infant.base import fetch_infant_template
 
 __all__ = [
     '_download_all_example_data', '_fake', 'brainstorm', 'eegbci',
-    'fetch_aparc_sub_parcellation', 'fetch_fsaverage',
+    'fetch_aparc_sub_parcellation', 'fetch_fsaverage', 'fetch_infant_template',
     'fetch_hcp_mmp_parcellation', 'fieldtrip_cmc', 'hf_sef', 'kiloword',
     'misc', 'mtrf', 'multimodal', 'opm', 'phantom_4dbti', 'sample',
     'sleep_physionet', 'somato', 'spm_face', 'testing', 'visual_92_categories',

diff --git a/mne/datasets/_fsaverage/base.py b/mne/datasets/_fsaverage/base.py
@@ -6,6 +6,7 @@
 import os.path as op
 
 
+from ..utils import _manifest_check_download, _get_path
 from ...utils import (verbose, get_subjects_dir, set_config)
 
 FSAVERAGE_MANIFEST_PATH = op.dirname(__file__)
@@ -64,38 +65,26 @@ def fetch_fsaverage(subjects_dir=None, verbose=None):
     # with open('fsaverage.txt', 'w') as fid:
     #     fid.write('\n'.join(names))
     #
-    from ..utils import _manifest_check_download
     subjects_dir = _set_montage_coreg_path(subjects_dir)
     subjects_dir = op.abspath(subjects_dir)
     fs_dir = op.join(subjects_dir, 'fsaverage')
     os.makedirs(fs_dir, exist_ok=True)
-
-    fsaverage_data_parts = {
-        'root.zip': dict(
-            url='https://osf.io/3bxqt/download?revision=2',
-            hash_='5133fe92b7b8f03ae19219d5f46e4177',
-            manifest=op.join(FSAVERAGE_MANIFEST_PATH, 'root.txt'),
-            destination=op.join(subjects_dir),
-        ),
-        'bem.zip': dict(
-            url='https://osf.io/7ve8g/download?revision=4',
-            hash_='b31509cdcf7908af6a83dc5ee8f49fb1',
-            manifest=op.join(FSAVERAGE_MANIFEST_PATH, 'bem.txt'),
-            destination=op.join(subjects_dir, 'fsaverage'),
-        ),
-    }
-    for fname, data in fsaverage_data_parts.items():
-        _manifest_check_download(
-            destination=data['destination'],
-            manifest_path=data['manifest'],
-            url=data['url'],
-            hash_=data['hash_'],
-        )
+    _manifest_check_download(
+        manifest_path=op.join(FSAVERAGE_MANIFEST_PATH, 'root.txt'),
+        destination=op.join(subjects_dir),
+        url='https://osf.io/3bxqt/download?revision=2',
+        hash_='5133fe92b7b8f03ae19219d5f46e4177',
+    )
+    _manifest_check_download(
+        manifest_path=op.join(FSAVERAGE_MANIFEST_PATH, 'bem.txt'),
+        destination=op.join(subjects_dir, 'fsaverage'),
+        url='https://osf.io/7ve8g/download?revision=4',
+        hash_='b31509cdcf7908af6a83dc5ee8f49fb1',
+    )
     return fs_dir
 
 
 def _get_create_subjects_dir(subjects_dir):
-    from ..utils import _get_path
     subjects_dir = get_subjects_dir(subjects_dir, raise_error=False)
     if subjects_dir is None:
         subjects_dir = _get_path(None, 'MNE_DATA', 'montage coregistration')

diff --git a/mne/datasets/_infant/ANTS1-0Months3T.txt b/mne/datasets/_infant/ANTS1-0Months3T.txt
@@ -0,0 +1,117 @@
+bem/ANTS1-0Months3T-5120-5120-5120-bem-sol.fif
+bem/ANTS1-0Months3T-5120-5120-5120-bem.fif
+bem/ANTS1-0Months3T-fiducials.fif
+bem/ANTS1-0Months3T-head.fif
+bem/ANTS1-0Months3T-oct-6-src.fif
+bem/ANTS1-0Months3T-vol-5-src.fif
+bem/inner_skull.surf
+bem/inner_skull_large.surf
+bem/outer_skin.surf
+bem/outer_skin_large.surf
+bem/outer_skull.surf
+bem/outer_skull_large.surf
+flirt_trans_mat.txt
+label/aparc.annot.ctab
+label/lh.aparc.a2009s.annot
+label/lh.aparc.annot
+label/lh.cortex.label
+label/rh.aparc.a2009s.annot
+label/rh.aparc.annot
+label/rh.cortex.label
+montages/10-10-montage.fif
+montages/10-10_electrodes.tsv
+montages/10-20-montage.fif
+montages/10-20_electrodes.tsv
+montages/10-5-montage.fif
+montages/10-5_electrodes.tsv
+montages/HGSN128-montage.fif
+montages/HGSN128_electrodes.tsv
+montages/HGSN129-montage.fif
+montages/HGSN129_electrodes.tsv
+mprage.nii.gz
+mri/T1.mgz
+mri/aparc+aseg.mgz
+mri/aseg.count.txt
+mri/aseg.mgz
+mri/aseg.nii.gz
+mri/aseg.presurf.mgz
+mri/brain.finalsurfs.mgz
+mri/brain.mgz
+mri/brain.nii.gz
+mri/brainmask.mgz
+mri/brainmask.nii.gz
+mri/filled.mgz
+mri/lh.dpial.ribbon.mgz
+mri/lh.dwhite.ribbon.mgz
+mri/lh.ribbon.mgz
+mri/norm.mgz
+mri/norm.nii.gz
+mri/rh.dpial.ribbon.mgz
+mri/rh.dwhite.ribbon.mgz
+mri/rh.ribbon.mgz
+mri/ribbon.mgz
+mri/transforms/niftyreg_affine.lta
+mri/transforms/niftyreg_affine.nii.gz
+mri/transforms/niftyreg_affine.txt
+mri/transforms/niftyreg_affine.xfm
+mri/transforms/talairach.auto.xfm
+mri/transforms/talairach.xfm
+mri/wm.mgz
+surf/10-10-montage.obj
+surf/10-10-montage.surf
+surf/10-20-montage.obj
+surf/10-20-montage.surf
+surf/10-5-montage.obj
+surf/10-5-montage.surf
+surf/HGSN128-montage.obj
+surf/HGSN128-montage.surf
+surf/fiducials.obj
+surf/fiducials.surf
+surf/lh.area
+surf/lh.curv
+surf/lh.defects
+surf/lh.inflated
+surf/lh.inflated.H
+surf/lh.inflated.K
+surf/lh.input
+surf/lh.orig
+surf/lh.orig.euler.txt
+surf/lh.orig_corrected
+surf/lh.pial
+surf/lh.qsphere
+surf/lh.qsphere.nofix
+surf/lh.smoothwm
+surf/lh.smoothwm1
+surf/lh.smoothwm2
+surf/lh.smoothwm3
+surf/lh.smoothwm4
+surf/lh.smoothwm5
+surf/lh.sphere
+surf/lh.sphere.reg
+surf/lh.sulc
+surf/lh.thickness
+surf/lh.white
+surf/rh.area
+surf/rh.curv
+surf/rh.defects
+surf/rh.inflated
+surf/rh.inflated.H
+surf/rh.inflated.K
+surf/rh.input
+surf/rh.orig
+surf/rh.orig.euler.txt
+surf/rh.orig_corrected
+surf/rh.pial
+surf/rh.qsphere
+surf/rh.qsphere.nofix
+surf/rh.smoothwm
+surf/rh.smoothwm1
+surf/rh.smoothwm2
+surf/rh.smoothwm3
+surf/rh.smoothwm4
+surf/rh.smoothwm5
+surf/rh.sphere
+surf/rh.sphere.reg
+surf/rh.sulc
+surf/rh.thickness
+surf/rh.white
diff --git a/mne/datasets/_infant/ANTS10-5Months3T.txt b/mne/datasets/_infant/ANTS10-5Months3T.txt
@@ -0,0 +1,115 @@
+bem/ANTS10-5Months3T-5120-5120-5120-bem-sol.fif
+bem/ANTS10-5Months3T-5120-5120-5120-bem.fif
+bem/ANTS10-5Months3T-fiducials.fif
+bem/ANTS10-5Months3T-head.fif
+bem/ANTS10-5Months3T-oct-6-src.fif
+bem/ANTS10-5Months3T-vol-5-src.fif
+bem/inner_skull.surf
+bem/inner_skull_large.surf
+bem/outer_skin.surf
+bem/outer_skin_large.surf
+bem/outer_skull.surf
+bem/outer_skull_large.surf
+flirt_trans_mat.txt
+label/aparc.annot.ctab
+label/lh.aparc.a2009s.annot
+label/lh.aparc.annot
+label/lh.cortex.label
+label/rh.aparc.a2009s.annot
+label/rh.aparc.annot
+label/rh.cortex.label
+montages/10-10-montage.fif
+montages/10-10_electrodes.tsv
+montages/10-20-montage.fif
+montages/10-20_electrodes.tsv
+montages/10-5-montage.fif
+montages/10-5_electrodes.tsv
+montages/HGSN128-montage.fif
+montages/HGSN128_electrodes.tsv
+montages/HGSN129-montage.fif
+montages/HGSN129_electrodes.tsv
+mprage.nii.gz
+mri/T1.mgz
+mri/aparc+aseg.mgz
+mri/aseg.count.txt
+mri/aseg.mgz
+mri/aseg.nii.gz
+mri/aseg.presurf.mgz
+mri/brain.finalsurfs.mgz
+mri/brain.mgz
+mri/brain.nii.gz
+mri/brainmask.mgz
+mri/brainmask.nii.gz
+mri/filled.mgz
+mri/lh.dpial.ribbon.mgz
+mri/lh.dwhite.ribbon.mgz
+mri/lh.ribbon.mgz
+mri/norm.mgz
+mri/norm.nii.gz
+mri/rh.dpial.ribbon.mgz
+mri/rh.dwhite.ribbon.mgz
+mri/rh.ribbon.mgz
+mri/ribbon.mgz
+mri/transforms/niftyreg_affine.lta
+mri/transforms/niftyreg_affine.nii.gz
+mri/transforms/niftyreg_affine.txt
+mri/transforms/niftyreg_affine.xfm
+mri/transforms/talairach.auto.xfm
+mri/transforms/talairach.xfm
+mri/wm.mgz
+surf/10-10-montage.obj
+surf/10-10-montage.surf
+surf/10-20-montage.obj
+surf/10-20-montage.surf
+surf/10-5-montage.obj
+surf/10-5-montage.surf
+surf/HGSN128-montage.obj
+surf/HGSN128-montage.surf
+surf/fiducials.obj
+surf/fiducials.surf
+surf/lh.area
+surf/lh.curv
+surf/lh.inflated
+surf/lh.inflated.H
+surf/lh.inflated.K
+surf/lh.orig
+surf/lh.orig.euler.txt
+surf/lh.orig_corrected
+surf/lh.pial
+surf/lh.qsphere
+surf/lh.qsphere.nofix
+surf/lh.smoothwm
+surf/lh.smoothwm1
+surf/lh.smoothwm2
+surf/lh.smoothwm3
+surf/lh.smoothwm4
+surf/lh.smoothwm5
+surf/lh.sphere
+surf/lh.sphere.reg
+surf/lh.sulc
+surf/lh.thickness
+surf/lh.white
+surf/rh.area
+surf/rh.curv
+surf/rh.defects
+surf/rh.inflated
+surf/rh.inflated.H
+surf/rh.inflated.K
+surf/rh.input
+surf/rh.orig
+surf/rh.orig.euler.txt
+surf/rh.orig_corrected
+surf/rh.pial
+surf/rh.qsphere
+surf/rh.qsphere.nofix
+surf/rh.smoothwm
+surf/rh.smoothwm1
+surf/rh.smoothwm2
+surf/rh.smoothwm3
+surf/rh.smoothwm4
+surf/rh.smoothwm5
+surf/rh.sphere
+surf/rh.sphere.reg
+surf/rh.sulc
+surf/rh.thickness
+surf/rh.white