ENH: Add qMRI example datasets

.github/workflows/validate_datasets.yml

@@ -13,12 +13,14 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
+        platform: [ubuntu-latest, macos-latest, windows-latest]
         bids-validator: [master, stable]
 
+    runs-on: ${{ matrix.platform }}
+
     env:
       TZ: Europe/Berlin
       FORCE_COLOR: 1
@@ -59,11 +61,11 @@ jobs:
         found=`find . -not -path "./.git*" -type f -size +500k`
         if [ "$found" == "" ]
         then
-          echo "No big files present, great!"
+            echo "No big files present, great!"
         else
-          echo "Found big files:"
-          echo "$found"
-          exit 1;
+            echo "Found big files:"
+            echo "$found"
+            exit 1;
         fi
       shell: bash
 
@@ -72,14 +74,30 @@ jobs:
         rc=0;
         for i in $(ls -d */ | grep -v node_modules);
         do
-          echo "Validating dataset" $i
-          if [ -f ${i%%/}/.SKIP_VALIDATION ]; then
-            echo "skipping validation for ${i%%/}"
-          elif [ -f ${i%%/}/.bids-validator-config.json ]; then
-            bids-validator ${i%%/} --ignoreNiftiHeaders || rc=$?
-          else
-            bids-validator ${i%%/} --ignoreNiftiHeaders -c $PWD/bidsconfig.json || rc=$?
-          fi
+            echo "Validating dataset" $i
+
+            if [ -f ${i%%/}/.SKIP_VALIDATION ]; then
+
+                echo "Skipping validation for ${i%%/}"
+
+            elif [ -f ${i%%/}/.bids-validator-config.json ]; then
+
+                bids-validator ${i%%/} --ignoreNiftiHeaders || rc=$?
+
+            else
+
+                if [ $i == "synthetic/" ]; then
+
+                    echo "Validating NIfTI headers for dataset" $i
+                    bids-validator ${i%%/} -c $PWD/bidsconfig.json || rc=$?
+
+                else
+
+                    bids-validator ${i%%/} --ignoreNiftiHeaders -c $PWD/bidsconfig.json || rc=$?
+
+                fi
+
+            fi
         done
         exit $rc;
       shell: bash

ds000246/CHANGES

@@ -1,4 +1,12 @@
-Revision history for OpenfMRI dataset ds000246
+1.0.1	2021-02-03
+
+	- Update some json files to conform with BIDS specs version 1.4.1
+
+ 1.0.0	2018-04-03
+
+	- Initial release at Open Neuro of the Brainstorm_Auditory_dataset
+
+  Revision history for OpenfMRI dataset ds000246
 
 1.0.0 2017-11-08
 

ds000246/README

@@ -1,4 +1,4 @@
-# DatasetAuditory - Brainstorm
+# Brainstorm - Auditory Dataset
 
 ## License
 
@@ -82,32 +82,3 @@ When correcting of delay #1, the process we use to detect the beginning of the t
 [3]: http://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize
 [4]: http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Pre-auricular_points_.28LPA.2C_RPA.29
 [5]: http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory
-
-
-### Comments added by Openfmri Curators ###
-===========================================
-
-General Comments
-----------------
-
-
-Defacing
---------
-Pydeface was used on all anatomical images to ensure de-identification of subjects. The code
-can be found at https://github.com/poldracklab/pydeface
-
-Quality Control
----------------
-MRIQC was run on the dataset. Results are located in derivatives/mriqc. Learn more about it here: https://mriqc.readthedocs.io/en/stable/
-
-Where to discuss the dataset
-----------------------------
-1) www.openfmri.org/dataset/ds000246/ See the comments section at the bottom of the dataset
-page.
-2) www.neurostars.org Please tag any discussion topics with the tags openfmri and ds000246.
-3) Send an email to submissions@openfmri.org. Please include the accession number in
-your email.
-
-Known Issues
-------------
-

ds000246/dataset_description.json

@@ -1,14 +1,20 @@
 {
-  "Name": "MEG-BIDS Brainstorm data sample",
-  "BIDSVersion": "1.0.2",
-  "License": "CC0",
-  "Authors": [
-    "Elizabeth Bock",
-    "Peter Donhauser",
-    "Francois Tadel",
-    "Sylvain Baillet"
+  "Name":"MEG-BIDS Brainstorm data sample",
+  "BIDSVersion":"1.4.1",
+  "License":"CC0",
+  "Authors":[
+      "Elizabeth Bock",
+      "Peter Donhauser",
+      "Francois Tadel",
+      "Guiomar Niso",
+      "Sylvain Baillet"
   ],
-  "HowToAcknowledge": "If you reference this dataset in your publications, please aknowledge its authors and cite Brainstorm as indicated on the website (http://neuroimage.usc.edu/brainstorm/CiteBrainstorm). Also, include the following message: ' This data was obtained from the OpenfMRI database. Its accession number is ds000246'",
-  "Funding": ["NIH (2R01EB009048-05)"],
-  "ReferencesAndLinks": ["https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090754", "http://neuroimage.usc.edu/brainstorm/", "https://openfmri.org/dataset/ds000246/"]
+  "HowToAcknowledge":"If you reference this dataset in your publications, please aknowledge its authors and cite Brainstorm as indicated on the website (http://neuroimage.usc.edu/brainstorm/CiteBrainstorm). \n\nAlso, include the following message: ' This data was obtained from the OpenNeuro database. Its accession number is ds000246'",
+  "Funding":["NIH (2R01EB009048-05)"],
+  "ReferencesAndLinks":[
+      "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090754",
+      "https://doi.org/10.3389/fnins.2019.00076",
+      "http://neuroimage.usc.edu/brainstorm/",
+      "https://openfmri.org/dataset/ds000246/"
+  ]
 }

ds000246/sub-emptyroom/meg/sub-emptyroom_task-noise_run-01_meg.json

@@ -1 +1,29 @@
-{"InstitutionName":"McConnell Brain Imaging Centre, McGill University","InstitutionAddress":"3801 University St., Montreal, QC, Canada","Manufacturer":"CTF","ManufacturersModelName":"CTF-275: OMEGA 2000","SoftwareVersions":"Acq 5.4.2-linux-20070507","TaskName":"noise","SamplingFrequency":2400,"PowerLineFrequency":60,"MEGChannelCount":274,"MEGREFChannelCount":26,"EEGChannelCount":0,"EOGChannelCount":0,"ECGChannelCount":0,"EMGChannelCount":0,"MiscChannelCount":0,"TriggerChannelCount":0,"DewarPosition":"Upright","SoftwareFilters":{"SpatialCompensation":{"GradientOrder":"3rd"}},"RecordingDuration":30,"RecordingType":"continuous","EpochLength":0,"ContinuousHeadLocalization":false,"DigitizedLandmarks":false,"DigitizedHeadPoints":false,"AssociatedEmptyRoom":"/sub-emptyroom/meg/sub-emptyroom_task-noise_run-01_meg.ds"}
+{
+    "InstitutionName":"McConnell Brain Imaging Centre, McGill University",
+    "InstitutionAddress":"3801 University St., Montreal, QC, Canada",
+    "Manufacturer":"CTF",
+    "ManufacturersModelName":"CTF-275: OMEGA 2000",
+    "SoftwareVersions":"Acq 5.4.2-linux-20070507",
+    "TaskName":"noise",
+    "SamplingFrequency":2400,
+    "PowerLineFrequency":60,
+    "MEGChannelCount":274,
+    "MEGREFChannelCount":26,
+    "EEGChannelCount":0,
+    "EOGChannelCount":0,
+    "ECGChannelCount":0,
+    "EMGChannelCount":0,
+    "MiscChannelCount":0,
+    "TriggerChannelCount":0,
+    "DewarPosition":"Upright",
+    "SoftwareFilters":{
+        "SpatialCompensation":{"GradientOrder":"3rd"}
+    },
+    "RecordingDuration":30,
+    "RecordingType":"continuous",
+    "EpochLength":0,
+    "ContinuousHeadLocalization":false,
+    "DigitizedLandmarks":false,
+    "DigitizedHeadPoints":false,
+    "AssociatedEmptyRoom":"/sub-emptyroom/meg/sub-emptyroom_task-noise_run-01_meg.ds"
+}

ds000247/CHANGES

@@ -1,3 +1,11 @@
+1.0.1	2021-02-03
+
+	- Update some json files to conform with BIDS specs version 1.4.1  
+
+1.0.0	2018-04-03
+
+	- Initial version of OMEGA_RestingState_sample
+
 Release history for OpenfMRI dataset ds000247
 
 1.0.0 2017-11-12

ds000247/README

@@ -48,33 +48,3 @@ The data in this dataset has been organized according to the BIDS specifications
 
 Release history:
 2016-12-01: initial release
-
-### Comments added by Openfmri Curators ###
-===========================================
-
-General Comments
-----------------
-
-
-Defacing
---------
-Pydeface was used on all anatomical images to ensure de-identification of subjects. The code
-can be found at https://github.com/poldracklab/pydeface
-mri_deface was used on all T1.mgz images located in derivatives. Learn more about it here:
-https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface
-
-Quality Control
----------------
-MRIQC could not be run on this dataset. It will be included in a future revision.
-
-Where to discuss the dataset
-----------------------------
-1) www.openfmri.org/dataset/ds000247/ See the comments section at the bottom of the dataset
-page.
-2) www.neurostars.org Please tag any discussion topics with the tags openfmri and ds000247.
-3) Send an email to submissions@openfmri.org. Please include the accession number in
-your email.
-
-Known Issues
-------------
-

ds000247/dataset_description.json

@@ -1,5 +1,5 @@
 {
-  "Name": "MEG-BIDS OMEGA sample",
+  "Name": "MEG-BIDS OMEGA RestingState_sample",
   "BIDSVersion": "1.0.2",
   "License": "CC0",
   "Authors": [
@@ -9,8 +9,10 @@
     "Francois Tadel",
     "Sylvain Baillet"
   ],
-  "HowToAcknowledge": "You are free to use all data in OMEGA for research purposes; please aknowledge its authors and cite the following reference in your publications if you have used data from OMEGA: Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S. OMEGA: The Open MEG Archive. Neuroimage. 2015; Available from: http://dx.doi.org/10.1016/j.neuroimage.2015.04.028. And please include the following message: 'This data was obtained from the OpenfMRI database. Its accession number is ds000247'",
-  "Funding": ["Quebec Bioimaging Network Strategic Initiative (QBIN 5886)"],
+  "HowToAcknowledge": "You are free to use all data in OMEGA for research purposes; please aknowledge its authors and cite the following reference in your publications if you have used data from OMEGA: Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S. OMEGA: The Open MEG Archive. Neuroimage. 2015; Available from: http://dx.doi.org/10.1016/j.neuroimage.2015.04.028. And please include the following message: 'This data was obtained from the OpenNeuro database. Its accession number is ds000247'",
+  "Funding": [
+    "Quebec Bioimaging Network Strategic Initiative (QBIN 5886)"
+  ],
   "ReferencesAndLinks": [
     "Niso G, Rogers C, Moreau JT, Chen LY, Madjar C, Das S, Bock E, Tadel F, Evans A, Jolicoeur P, Baillet S. OMEGA: The Open MEG Archive. Neuroimage. 2015; Available from: http://dx.doi.org/10.1016/j.neuroimage.2015.04.028",
     "https://openfmri.org/dataset/ds000247/", 

ds000247/sub-0002/ses-0001/meg/sub-0002_ses-0001_task-rest_run-01_meg.json

@@ -1 +1,29 @@
-{"InstitutionName":"McConnell Brain Imaging Centre, McGill University","InstitutionAddress":"3801 University St., Montreal, QC, Canada","Manufacturer":"CTF","ManufacturersModelName":"CTF-275: OMEGA 2000","SoftwareVersions":"Acq 5.4.2-linux-20070507","TaskName":"rest","SamplingFrequency":2400,"PowerLineFrequency":60,"MEGChannelCount":270,"MEGREFChannelCount":26,"EEGChannelCount":0,"EOGChannelCount":2,"ECGChannelCount":1,"EMGChannelCount":0,"MiscChannelCount":0,"TriggerChannelCount":0,"DewarPosition":"Upright","SoftwareFilters":{"SpatialCompensation":{"GradientOrder":"3rd"}},"RecordingDuration":600,"RecordingType":"continuous","EpochLength":0,"ContinuousHeadLocalization":false,"DigitizedLandmarks":false,"DigitizedHeadPoints":true,"AssociatedEmptyRoom":"/sub-emptyroom/ses-18901014/meg/sub-emptyroom_ses-18901014_task-noise_run-01_meg.ds"}
+{
+    "InstitutionName":"McConnell Brain Imaging Centre, McGill University",
+    "InstitutionAddress":"3801 University St., Montreal, QC, Canada",
+    "Manufacturer":"CTF",
+    "ManufacturersModelName":"CTF-275: OMEGA 2000",
+    "SoftwareVersions":"Acq 5.4.2-linux-20070507",
+    "TaskName":"rest",
+    "SamplingFrequency":2400,
+    "PowerLineFrequency":60,
+    "MEGChannelCount":270,
+    "MEGREFChannelCount":26,
+    "EEGChannelCount":0,
+    "EOGChannelCount":2,
+    "ECGChannelCount":1,
+    "EMGChannelCount":0,
+    "MiscChannelCount":0,
+    "TriggerChannelCount":0,
+    "DewarPosition":"Upright",
+    "SoftwareFilters": {
+        "SpatialCompensation":{"GradientOrder":"3rd"}
+        },
+    "RecordingDuration":600,
+    "RecordingType":"continuous",
+    "EpochLength":0,
+    "ContinuousHeadLocalization":false,
+    "DigitizedLandmarks":false,
+    "DigitizedHeadPoints":true,
+    "AssociatedEmptyRoom":"/sub-emptyroom/ses-18901014/meg/sub-emptyroom_ses-18901014_task-noise_run-01_meg.ds"
+}

ds000247/sub-0003/ses-0001/meg/sub-0003_ses-0001_task-rest_run-01_meg.json

@@ -1 +1,31 @@
-{"InstitutionName":"McConnell Brain Imaging Centre, McGill University","InstitutionAddress":"3801 University St., Montreal, QC, Canada","Manufacturer":"CTF","ManufacturersModelName":"CTF-275: OMEGA 2000","SoftwareVersions":"Acq 5.4.2-linux-20070507","TaskName":"rest","SamplingFrequency":2400,"PowerLineFrequency":60,"MEGChannelCount":270,"MEGREFChannelCount":26,"EEGChannelCount":0,"EOGChannelCount":2,"ECGChannelCount":1,"EMGChannelCount":0,"MiscChannelCount":0,"TriggerChannelCount":0,"DewarPosition":"Upright","SoftwareFilters":{"SpatialCompensation":{"GradientOrder":"3rd"}},"RecordingDuration":600,"RecordingType":"continuous","EpochLength":0,"ContinuousHeadLocalization":false,"DigitizedLandmarks":false,"DigitizedHeadPoints":true,"AssociatedEmptyRoom":"sub-emptyroom/ses-18901015/meg/sub-emptyroom_ses-18901015_task-noise_run-01_meg.ds"}
+{
+    "InstitutionName":"McConnell Brain Imaging Centre, McGill University",
+    "InstitutionAddress":"3801 University St., Montreal, QC, Canada",
+    "Manufacturer":"CTF",
+    "ManufacturersModelName":"CTF-275: OMEGA 2000",
+    "SoftwareVersions":"Acq 5.4.2-linux-20070507",
+    "TaskName":"rest",
+    "SamplingFrequency":2400,
+    "PowerLineFrequency":60,
+    "MEGChannelCount":270,
+    "MEGREFChannelCount":26,
+    "EEGChannelCount":0,
+    "EOGChannelCount":2,
+    "ECGChannelCount":1,
+    "EMGChannelCount":0,
+    "MiscChannelCount":0,
+    "TriggerChannelCount":0,
+    "DewarPosition":"Upright",
+    "SoftwareFilters":{
+       "SpatialCompensation":{
+          "GradientOrder":"3rd"
+       }
+    },
+    "RecordingDuration":600,
+    "RecordingType":"continuous",
+    "EpochLength":0,
+    "ContinuousHeadLocalization":false,
+    "DigitizedLandmarks":false,
+    "DigitizedHeadPoints":true,
+    "AssociatedEmptyRoom":"sub-emptyroom/ses-18901015/meg/sub-emptyroom_ses-18901015_task-noise_run-01_meg.ds"
+ }

ds000247/sub-0004/ses-0001/meg/sub-0004_ses-0001_task-rest_run-01_meg.json

@@ -1 +1,37 @@
-{"InstitutionName":"McConnell Brain Imaging Centre, McGill University","InstitutionAddress":"3801 University St., Montreal, QC, Canada","Manufacturer":"CTF","ManufacturersModelName":"CTF-275: OMEGA 2000","SoftwareVersions":"Acq 5.4.2-linux-20070507","TaskName":"rest","SamplingFrequency":2400,"PowerLineFrequency":60,"MEGChannelCount":270,"MEGREFChannelCount":26,"EEGChannelCount":0,"EOGChannelCount":2,"ECGChannelCount":1,"EMGChannelCount":0,"MiscChannelCount":0,"TriggerChannelCount":0,"DewarPosition":"Upright","SoftwareFilters":{"SpatialCompensation":{"GradientOrder":"3rd"}},"RecordingDuration":599,"RecordingType":"continuous","EpochLength":0,"ContinuousHeadLocalization":true,"HeadCoilFrequency":[1470,1530,1590],"MaxMovement":0.002962763321630642,"DigitizedLandmarks":false,"DigitizedHeadPoints":true,"AssociatedEmptyRoom":"sub-emptyroom/ses-18910303/meg/sub-emptyroom_ses-18910303_task-noise_run-01_meg.ds"}
+{
+    "InstitutionName":"McConnell Brain Imaging Centre, McGill University",
+    "InstitutionAddress":"3801 University St., Montreal, QC, Canada",
+    "Manufacturer":"CTF",
+    "ManufacturersModelName":"CTF-275: OMEGA 2000",
+    "SoftwareVersions":"Acq 5.4.2-linux-20070507",
+    "TaskName":"rest",
+    "SamplingFrequency":2400,
+    "PowerLineFrequency":60,
+    "MEGChannelCount":270,
+    "MEGREFChannelCount":26,
+    "EEGChannelCount":0,
+    "EOGChannelCount":2,
+    "ECGChannelCount":1,
+    "EMGChannelCount":0,
+    "MiscChannelCount":0,
+    "TriggerChannelCount":0,
+    "DewarPosition":"Upright",
+    "SoftwareFilters":{
+       "SpatialCompensation":{
+          "GradientOrder":"3rd"
+       }
+    },
+    "RecordingDuration":599,
+    "RecordingType":"continuous",
+    "EpochLength":0,
+    "ContinuousHeadLocalization":true,
+    "HeadCoilFrequency":[
+       1470,
+       1530,
+       1590
+    ],
+    "MaxMovement":0.002962763321630642,
+    "DigitizedLandmarks":false,
+    "DigitizedHeadPoints":true,
+    "AssociatedEmptyRoom":"sub-emptyroom/ses-18910303/meg/sub-emptyroom_ses-18910303_task-noise_run-01_meg.ds"
+ }