Merge branch 'bids-standard:master' into fnirstapping

qmri_mp2rage/sub-1/anat/sub-1_inv-1_MP2RAGE.json

@@ -4,5 +4,5 @@
   "RepetitionTimeExcitation": 0.0062,
   "RepetitionTimePreparation": 5.5,
   "NumberShots": 159,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rage/sub-1/anat/sub-1_inv-2_MP2RAGE.json

@@ -4,5 +4,5 @@
   "RepetitionTimeExcitation": 0.0062,
   "RepetitionTimePreparation": 5.5,
   "NumberShots": 159,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rageme/sub-1/anat/sub-1_echo-1_inv-2_MP2RAGE.json

@@ -5,5 +5,5 @@
   "RepetitionTimePreparation": 6.723,
   "NumberShots": 150,
   "EchoTime": 0.006,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rageme/sub-1/anat/sub-1_echo-2_inv-2_MP2RAGE.json

@@ -5,5 +5,5 @@
   "RepetitionTimePreparation": 6.723,
   "NumberShots": 150,
   "EchoTime": 0.0145,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rageme/sub-1/anat/sub-1_echo-3_inv-2_MP2RAGE.json

@@ -5,5 +5,5 @@
   "RepetitionTimePreparation": 6.723,
   "NumberShots": 150,
   "EchoTime": 0.023,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rageme/sub-1/anat/sub-1_echo-4_inv-2_MP2RAGE.json

@@ -5,5 +5,5 @@
   "RepetitionTimePreparation": 6.723,
   "NumberShots": 150,
   "EchoTime": 0.0315,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

qmri_mp2rageme/sub-1/anat/sub-1_inv-1_MP2RAGE.json

@@ -4,5 +4,5 @@
   "RepetitionTimeExcitation": 0.0062,
   "RepetitionTimePreparation": 6.723,
   "NumberShots": 150,
-  "FieldStrength": 7
+  "MagneticFieldStrength": 7
 }

synthetic/README

@@ -0,0 +1,16 @@
+# BIDS synthetic dataset
+
+## Summary
+
+- 113 Files
+- 5 - Subjects
+- 2 - Sessions
+
+Available Tasks
+
+- N-Back
+- Rest
+
+Available Modalities
+
+- MRI

synthetic/code/create_synthethic_ds.sh

@@ -3,39 +3,36 @@
 # small bash script to create a synthethic BIDS data set
 
 # defines where the BIDS data set will be created
-start_dir=`pwd` 
+start_dir=$(pwd)
 raw_dir=${start_dir}/../
 
 subject_list='01 02 03 04 05'
-session_list='01' 
+session_list='01'
 
-create_raw_beh () {
+create_raw_beh() {
 
-	target_dir=$1
-	subject=$2
-	ses=$3
+    target_dir=$1
+    subject=$2
+    ses=$3
 
-	suffix='_beh'
-	task_name='stroop'
+    suffix='_beh'
+    task_name='stroop'
 
-	this_dir=${target_dir}/sub-${subject}/ses-${ses}/beh
+    this_dir=${target_dir}/sub-${subject}/ses-${ses}/beh
 
-	mkdir -p ${this_dir}
+    mkdir -p ${this_dir}
 
-	filename=${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}${suffix}.tsv
-	echo "trial\tresponse\treaction_time\tstim_file" > ${filename}
-	echo "congruent\tred\t1.435\timages/word-red_color-red.jpg"  >> ${filename}
-	echo "incongruent\tred\t1.739\timages/word-red_color-blue.jpg" >> ${filename}
+    filename=${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}${suffix}.tsv
+    echo "trial\tresponse\treaction_time\tstim_file" >${filename}
+    echo "congruent\tred\t1.435\timages/word-red_color-red.jpg" >>${filename}
+    echo "incongruent\tred\t1.739\timages/word-red_color-blue.jpg" >>${filename}
 
 }
 
-
 # RAW DATASET
-for subject in ${subject_list}
-do
-	for ses in ${session_list}
-	do
-		create_raw_beh ${raw_dir} ${subject} ${ses}
-	done
+for subject in ${subject_list}; do
+    for ses in ${session_list}; do
+        create_raw_beh ${raw_dir} ${subject} ${ses}
+    done
 
 done

synthetic/dataset_description.json

@@ -1,6 +1,10 @@
 {
 	"Name": "Synthetic dataset for inclusion in BIDS-examples",
-	"BIDSVersion": "1.0.2",
+	"BIDSVersion": "1.6",
+	"DatasetType": "raw",
 	"License": "PD",
-	"Authors": ["Markiewicz, C. J."]
-}
+	"Authors": [
+		"Markiewicz, C. J.",
+		"Gau, Rémi"
+	]
+}

synthetic/derivatives/fmriprep/.bidsignore

@@ -0,0 +1 @@
+*_confounds.tsv

synthetic/derivatives/fmriprep/CHANGES

@@ -0,0 +1,5 @@
+1.0.1 2021-10-22
+  - Make BIDS derivative compatible
+
+1.0.0 2018-02-02
+  - Initial release.

synthetic/derivatives/fmriprep/README

@@ -0,0 +1 @@
+# README

synthetic/derivatives/fmriprep/dataset_description.json

@@ -0,0 +1,22 @@
+{
+    "Name": "fMRIPrep - fMRI PREProcessing workflow",
+    "BIDSVersion": "1.6.0",
+    "DatasetType": "derivative",
+    "GeneratedBy": [
+        {
+            "Name": "fMRIPrep",
+            "Version": "1.0.6",
+            "CodeURL": "https://github.com/nipreps/fmriprep/archive/refs/tags/1.0.6.tar.gz"
+        },
+        {
+            "Name": "Manual",
+            "Description": "Adjusted to conform to BIDS Derivatives"
+        }
+    ],
+    "SourceDatasets": [
+        {
+            "URL": "../.."
+        }
+    ],
+    "HowToAcknowledge": "Please cite our paper (https://doi.org/10.1038/s41592-018-0235-4), and include the generated citation boilerplate within the Methods section of the text."
+}

synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json

@@ -0,0 +1,7 @@
+{
+  "RawSources": [
+    "sub-01/ses-01/sub-01_ses-01_task-nback_run-01_bold.nii"
+  ],
+  "TaskName": "N-Back",
+  "RepetitionTime": 2.5
+}

synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-01_space-T1w_desc-preproc_bold.json

@@ -0,0 +1,7 @@
+{
+  "RawSources": [
+    "sub-01/ses-01/sub-01_ses-01_task-nback_run-01_bold.nii"
+  ],
+  "TaskName": "N-Back",
+  "RepetitionTime": 2.5
+}

synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json

@@ -0,0 +1,7 @@
+{
+  "RawSources": [
+    "sub-01/ses-01/sub-01_ses-01_task-nback_run-02_bold.nii"
+  ],
+  "TaskName": "N-Back",
+  "RepetitionTime": 2.5
+}

synthetic/derivatives/fmriprep/sub-01/ses-01/func/sub-01_ses-01_task-nback_run-02_space-T1w_desc-preproc_bold.json

@@ -0,0 +1,7 @@
+{
+  "RawSources": [
+    "sub-01/ses-01/sub-01_ses-01_task-nback_run-02_bold.nii"
+  ],
+  "TaskName": "N-Back",
+  "RepetitionTime": 2.5
+}