Mindboggle-101: 101 human brain MRI volumes and surfaces, derived templates, and anatomically labeled atlases
Year: 2016
Type: other
Abstract: README Individually labeled cortical surfaces and brain volumes from magnetic resonance images of 101 healthy individuals, together with the atlases and templates derived from them, and the labeling protocol they follow. This is the core Mindboggle-101 dataset. Companion records hold the OASIS-TRT-20 whole-brain (subcortical) labels, which carry a more restrictive license, and the bulk processed output. Citation 101 labeled brain images and a consistent human cortical labeling protocol. Arno Klein, Jason Tourville. Frontiers in Brain Imaging Methods. 6:171 (2012). DOI: 10.3389/fnins.2012.00171 Contents Mindboggle101_release3/ The official Mindboggle-101 release 3 (updated 2019-04-03). Labeled surfaces (vtk) and volumes (nii.gz) for each scanned group -- OASIS-TRT-20, NKI-TRT-20, NKI-RS-22, MMRR-21, HLN-12, Extra-18 and others. Brains are provided in their original space and affine-registered to MNI152 space. Grouped as one archive per cohort to stay within Zenodo's 100-file limit. Mindboggle101_atlases/ Surface and volume brain atlases: anatomical labels derived from a population of brains. Volume atlases were built with the joint fusion algorithm (Hongzhi Wang, 2013; distributed with ANTs) over the 20 OASIS-TRT brains, after antsRegistration warped them to the OASIS-30 Atropos template. Results are given in OASIS-30 space, in MNI152 space, and resampled to 2mm^3. OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_{OASIS-30,MNI152,MNI152_2mm}_v2.nii.gz OASIS-TRT-20_jointfusion_DKT31_CMA_label_probabilities_in_{OASIS-30,MNI152}_v2.nii.gz [lh,rh].DKT31atlas101subjects.gcs -- FreeSurfer classifier, all 101 participants (2016) [lh,rh].DKTatlas40.gcs -- FreeSurfer classifier, 40 participants (2012) code.zip -- scripts referenced below Mindboggle101_templates/ Unlabeled reference images, each built by combining images from multiple subjects. ANTs brain volume templates were made with buildtemplateparallel.sh, head volume templates with antsMultivariateTemplateConstruction.sh, and FreeSurfer surface templates with make_freesurfer_template.txt. Head_VolumeTemplate_[GROUP].nii.gz Brain_VolumeTemplate_[GROUP].nii.gz Brain_VolumeTemplate_[GROUP]_MNI152space.nii.gz Brain_VolumeTemplate_[GROUP]_MNI152space_2mm.nii.gz Brain_VolumeTemplate_[GROUP]_MNI152space_affine.txt SurfaceTemplate_[GROUP]/ -- cortical surfaces SurfaceTemplate_Mindboggle-101/ -- N=101 cortical surfaces These templates are multi-subject averages. No individual is identifiable from them, including the head (non-brain-extracted) templates. DKT_labeling_protocol/ The Desikan-Killiany-Tourville cortical labeling protocol. DKT_classifier_evaluation/ 2012 Evaluation of DKT labeling protocol through the use of a FreeSurfer-style Gaussian classifier (Klein and Tourville, 2012). docs/ Subject tables, scan sources, changelogs and supporting scripts. CHANGELOG.txt -- log of changes label_definitions.txt -- labeling protocol (see article above) labels_on_fsaverage_surfaces.png -- example labels subject_list_Mindboggle101.txt -- list of subjects subject_sources_Mindboggle101.txt -- scan sources subject_table_Mindboggle101.pdf -- table of subjects code.zip -- contains code_prep_WholeBrain_OASIS-TRT-20_labels.txt, code_postprocess_Mindboggle101_data.txt, code_resample2mm.txt, make_jointfusion_atlas.txt, make_freesurfer_classifier_atlas.txt, resample2mm.txt License CC BY 4.0. See LICENSE. The Mindboggle-101 collection Mindboggle-101 is published as multiple Zenodo records. They are split by license and by size. # Record Contents License DOI 1 Mindboggle-101 dataset (this record) Labeled brains, atlases, templates, DKT protocol CC BY 4.0 10.5281/zenodo.22070005 2 OASIS-TRT-20 whole-brain labels Manually labeled subcortical structures, 20 brains CC BY-NC-ND 4.0 10.5281/zenodo.22071825 3 antsCorticalThickness output ANTs cortical thickness pipeline output CC BY 4.0 10.5281/zenodo.22071936 4 FreeSurfer output FreeSurfer recon-all output CC BY 4.0 10.5281/zenodo.22072032 5 Mindboggle output Mindboggle shape/feature output, DKT classifier evaluation CC BY 4.0 10.5281/zenodo.22072081 Start with record 1. It contains the labeled brains, atlases and templates, and is the record to cite for most purposes. Record 2 is separated only because its license is more restrictive. Records 3-5 are bulk pipeline output, derived from record 1 and regenerable from it with the named software. All records share the citation above and are grouped in the Mindboggle-101 Zenodo community. Provenance of the imaging data The magnetic resonance images underlying Mindboggle-101 include data acquired by other projects. Please cite the originating project alongside the article above: Nathan Kline Institute (NKI) Open Access Series of Imaging Studies (OASIS) Multi-Modal Reproducibility Resource (Johns Hopkins / Kirby) Colin27 single-subject MNI template See docs/subject_sources_Mindboggle101.txt in record 1 for the per-subject mapping.
Author: Klein, Arno
Institution: Child Mind Institute
Language: English
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7204093335