BEP038: Atlas examples

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
 skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
 builtin = clear,rare
-ignore-words-list = nd,te
+ignore-words-list = nd,te,Sepulcre

.github/workflows/validate_datasets.yml

@@ -2,12 +2,10 @@ name: validate_datasets
 
 on:
   push:
-    branches: ['**']
+    branches: [master, main]
+    tags: ['*']
   pull_request:
-    branches: ['**']
-  create:
-    branches: [master]
-    tags: ['**']
+    branches: [master, main, 'bep*']
   schedule:
     - cron: "0 4 * * 1"
   workflow_dispatch:
@@ -77,6 +75,7 @@ jobs:
       run: |
         git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
         cd ../bids-validator
+        git checkout bep038
         deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
 
     - name: Install BIDS validator (legacy)
@@ -97,7 +96,7 @@ jobs:
       if: "matrix.bids-validator == 'stable'"
       run: |
         echo "Checking for big files ..."
-        found=`find . -not -path "./.git*" -type f -size +500k`
+        found=`find . -not -path "./.git*" -type f -size +1M`
         if [ "$found" == "" ]
         then
             echo "No big files present, great!"
@@ -108,7 +107,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -120,7 +119,7 @@ jobs:
     - name: Skip main validation for datasets with unreleased spec features
       # Replace ${EMPTY} with dataset patterns, when this is needed
       # Reset to "for DS in ${EMPTY}; ..." after a spec release
-      run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in dwi_deriv pheno004 atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -129,7 +128,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--1714.org.readthedocs.build/en/1714/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

atlas-4S/README.md

@@ -0,0 +1,8 @@
+# A derivative using the 4S (Schaefer Supplemented with Subcortical Structures) atlas
+
+This example includes atlas segmentations resampled into subject-specific spaces and/or resolutions.
+
+The `sourcedata/atlas-4S` subdirectory contains the atlas files used to generate these derivatives.
+
+Because this derivative dataset uses the `atlas-4S` entity,
+a copy of the `atlas-4S_description.json` from the source atlas is also distributed.

atlas-4S/atlas-4S_description.json

@@ -0,0 +1,142 @@
+{
+    "Authors": [
+        "M. Cieslak",
+        "T. Salo",
+        "E. Feczko",
+        "T.D. Satterthwaite"
+    ],
+    "Curators": [
+        "M. Cieslak",
+        "T. Salo",
+        "E. Feczko",
+        "T.D. Satterthwaite"
+    ],
+    "Description": "A set of non-cortical atlases and the Schaefer cortical atlas, that have been merged together in template space.",
+    "LevelType": "atlas",
+    "License": "CC BY-ND",
+    "Name": "4S: Schaefer Supplemented with Subcortical Structures",
+    "ReferencesAndLinks": [
+        "https://github.com/PennLINC/AtlasPack"
+    ],
+    "SampleSize": 0,
+    "SourceAtlases": {
+        "CIT168Subcortical": {
+            "Authors": [
+                "W.M. Pauli",
+                "A.N. Nili",
+                "J.M. Tyszka"
+            ],
+            "Curators": [
+                "W.M. Pauli",
+                "A.N. Nili",
+                "J.M. Tyszka",
+                "M. Okamoto"
+            ],
+            "Description": "Parcellations based on high spatial resolution, three-dimensional templates, using high-accuracy diffeomorphic registration of T1- and T2- weighted structural images from 168 typical adults between 22 and 35 years old. NOTE: Atlases originally assigned the same label to structures in each hemisphere. Here we have split the regions into hemispheres. Additionally, the SNC, PBP and VTA regions have been merged into a single structure.",
+            "License": "MIT: https://github.com/jmtyszka/CIT168-SubCorticalAtlas/blob/master/LICENSE.md",
+            "Name": "CIT168",
+            "ReferencesAndLinks": [
+                "https://neurovault.org/collections/3145/",
+                "https://osf.io/jkzwp/wiki/home/",
+                "https://github.com/jmtyszka/CIT168-SubCorticalAtlas",
+                "Pauli, W., Nili, A. & Tyszka, J. A high-resolution probabilistic in vivo atlas of human subcortical brain nuclei. Sci Data 5, 180063 (2018). https://doi.org/10.1038"
+            ]
+        },
+        "Cerebellum": {
+            "Authors": [
+                "King, M.",
+                "Hernandez-Castillo, C.R.",
+                "Poldrack, R.R.",
+                "Ivry, R.",
+                "Diedrichsen, J."
+            ],
+            "Curators": [
+                "Diedrichsen J"
+            ],
+            "Description": "King et al. (2019) provided an extensive characterization of the functional organization of the cerebellum of 24 healthy, young participants. The contrast are for for 47 task conditions, accounted for the activity caused by left hand, right hand, and eye movements. All contrast maps are relative to the mean activity across all tasks. The parcellation into 10 regions is defined from the task-evoked activity across all tasks.",
+            "License": "Creative Commons license CC BY-ND (Attribution - No derivatives)",
+            "Name": "Multi-domain task battery (MDTB) cerebellar parcellation",
+            "ReferencesAndLinks": [
+                "https://github.com/DiedrichsenLab/cerebellar_atlases",
+                "King, M., Hernandez-Castillo, C.R., Poldrack, R.R., Ivry, R., and Diedrichsen, J. (2019). Functional Boundaries in the Human Cerebellum revealedby a Multi-Domain Task Battery. Nat. Neurosci."
+            ]
+        },
+        "HCPSubcortical": {
+            "Authors": [
+                "M.F. Glasser",
+                "S.N. Sotiropoulos",
+                "J.A. Wilson",
+                "T.S. Coalson",
+                "B. Fischl",
+                "J.L. Andersson",
+                "J. Xu",
+                "S. Jbabdi",
+                "M. Webster",
+                "J.R. Polimeni",
+                "D.C. Van Essen",
+                "M. Jenkinson",
+                "The WU-Minn HCP Consortium"
+            ],
+            "Description": "The hippocampus and amygdala regions from the HCP subcortical atlas were selected.",
+            "License": "https://github.com/Washington-University/HCPpipelines/blob/21c0867c7f3a59554b9e28f5fe5cddd41e159170/LICENSE.md",
+            "Name": "HCP Subcortical Parcellation",
+            "ReferencesAndLinks": [
+                "https://github.com/Washington-University/HCPpipelines/blob/21c0867c7f3a59554b9e28f5fe5cddd41e159170/global/templates/170494_Greyordinates/Atlas_ROIs.1.60.nii.gz",
+                "Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B., Andersson, J. L., ... & Wu-Minn HCP Consortium. (2013). The minimal preprocessing pipelines for the Human Connectome Project. Neuroimage, 80, 105-124."
+            ]
+        },
+        "Schaefer2018v0143": {
+            "Authors": [
+                "A Schaefer",
+                "R Kong",
+                "E.M. Gordon",
+                "T.O. Laumann",
+                "X. Zuo",
+                "A.J. Holmes",
+                "S.B. Eickhoff",
+                "B.T. Yeo"
+            ],
+            "Curators": [
+                "A Schaefer",
+                "R Kong",
+                "E.M. Gordon",
+                "T.O. Laumann",
+                "X. Zuo",
+                "A.J. Holmes",
+                "S.B. Eickhoff",
+                "B.T. Yeo"
+            ],
+            "Description": "Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels. More details can be found in Schaefer et al. 2018.",
+            "License": "MIT: https://github.com/ThomasYeoLab/CBIG/blob/a8c7a0bb845210424ef1c46d1435fec591b2cf3d/LICENSE.md",
+            "Name": "Schaefer2018v0143",
+            "ReferencesAndLinks": [
+                "https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal",
+                "Schaefer, A., Kong, R., Gordon, E. M., Laumann, T. O., Zuo, X. N., Holmes, A. J., Eickhoff, S. B., & Yeo, B. T. (2018). Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI. Cerebral cortex, 28(9), 3095-3114."
+            ]
+        },
+        "ThalamusHCP": {
+            "Authors": [
+                "E. Najdenovska",
+                "Y. Al\u00e9man-G\u00f3mez",
+                "G. Battistella",
+                "M. Descoteaux",
+                "P. Hagmann",
+                "S. Jacquemont",
+                "P. Maeder",
+                "J.P. Thiran",
+                "E. Fornari",
+                "M. Bach Cuadra"
+            ],
+            "Description": "Regions are based on a probabilistic atlas of anatomical subparts of the thalamus built upon a relatively large dataset where the individual thalamic parcellation was done by employing a recently proposed automatic diffusion-based clustering method.",
+            "License": "Creative Commons Attribution Share Alike 4.0 International https://creativecommons.org/licenses/by-sa/4.0/legalcode",
+            "Name": "HCP Thalamic Parcellation",
+            "ReferencesAndLinks": [
+                "doi: 10.1038/sdata.2018.270",
+                "https://zenodo.org/record/1405484/files/Thalamus_Nuclei-HCP-MaxProb.nii.gz",
+                "https://zenodo.org/record/1405484/files/Thalamic_Nuclei-ColorLUT.txt",
+                "Najdenovska, E., Alem\u00e1n-G\u00f3mez, Y., Battistella, G. et al. In-vivo probabilistic atlas of human thalamic nuclei based on diffusion-weighted magnetic resonance imaging. Sci Data 5, 180270 (2018). https://doi.org/10.1038/sdata.2018.270"
+            ]
+        }
+    },
+    "Species": "Human"
+}

atlas-4S/dataset_description.json

@@ -0,0 +1,35 @@
+{
+    "Authors": [
+        "M. Cieslak",
+        "T. Salo",
+        "E. Feczko",
+        "T.D. Satterthwaite"
+    ],
+    "BIDSVersion": "1.10.1",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "AtlasPack",
+            "CodeURL": "https://github.com/PennLINC/AtlasPack"
+        }
+    ],
+    "License": "CC BY-ND",
+    "Name": "4S: Schaefer Supplemented with Subcortical Structures",
+    "SourceDatasets": [
+        {
+            "URL": "https://github.com/jmtyszka/CIT168-SubCorticalAtlas"
+        },
+        {
+            "URL": "https://github.com/DiedrichsenLab/cerebellar_atlases"
+        },
+        {
+            "URL": "https://github.com/Washington-University/HCPpipelines/blob/21c0867c7f3a59554b9e28f5fe5cddd41e159170/global/templates/170494_Greyordinates/Atlas_ROIs.1.60.nii.gz"
+        },
+        {
+            "URL": "https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal"
+        },
+        {
+            "URL": "https://zenodo.org/record/1405484/files/Thalamus_Nuclei-HCP-MaxProb.nii.gz"
+        }
+    ]
+}

atlas-4S/sourcedata/atlas-4S/README.md

@@ -0,0 +1,6 @@
+# 4S:S chaefer Supplemented with Subcortical Structures
+
+This repository contains two resolutions (156, 256) of the 4S atlas,
+which is the Schaefer 2018 cortical atlas supplemented with subcortical structures from other atlases.
+
+The atlas is shared in MNI152NLin6Asym, MNI152NLin2009cAsym, MNIInfant:cohort-1, MNIInfant:cohort-2, and fsLR space.