[DATALAD RUNCMD] ./.recreate_hierarchy

=== Do not change lines below === { "chain": [], "cmd": "./.recreate_hierarchy", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "proj-nipoppy" } ^^^ Do not change lines above ^^^
bids-standard · Sep 6, 2024 · 648a57d · 648a57d
1 parent fb9553f
commit 648a57d
Show file tree

Hide file tree

Showing 15 changed files with 34 additions and 0 deletions.
diff --git a/proj-nipoppy/CHANGES b/proj-nipoppy/CHANGES
@@ -0,0 +1,4 @@
+0.0.1 2024-06-20
+
+  -  Started to work on this support of the DatasetType project
+
diff --git a/proj-nipoppy/README.md b/proj-nipoppy/README.md
@@ -0,0 +1,13 @@
+This is an example of an entire project/study level BIDS dataset.
+Built taking a hierarchy depicted on
+https://github.com/neurodatascience/nipoppy?tab=readme-ov-file#nipoppy
+and turning it into a valid BIDS layout.
+
+Some files (e.g. bagel.csv) are specific to nipoppy etc projects, but since
+located under folders where bids layout is not enforced -- should be just fine. 
+
+Some outstanding issues with validator(s) which were ran into while trying to
+get "proper" validation working using deno bids-validator (mark when solved)
+
+- [ ] https://github.com/bids-standard/bids-validator/issues/2007
+
diff --git a/proj-nipoppy/code/global_config.json b/proj-nipoppy/code/global_config.json
@@ -0,0 +1 @@
+{}
diff --git a/proj-nipoppy/dataset_description.json b/proj-nipoppy/dataset_description.json
@@ -0,0 +1,9 @@
+{
+    "Name": "Example how nipoppy dataset could be presented as project-type BIDS dataset",
+	"Description": "Demonstration for the https://github.com/bids-standard/bids-specification/pull/1861",
+    "BIDSVersion": "1.10.0",
+    "DatasetType": "project",
+    "Authors": [
+        "Yaroslav O. Halchenko", "Samuel Nastase"
+    ]
+}
diff --git a/proj-nipoppy/derivatives/bagel.csv b/proj-nipoppy/derivatives/bagel.csv
@@ -0,0 +1,4 @@
+bids_id,participant_id,session,has_mri_data,pipeline_name,pipeline_version,pipeline_starttime,pipeline_complete
+sub-MNI001,MNI001,1,TRUE,freesurfer,6.0.1,2022-05-24 13:43,SUCCESS
+sub-MNI001,MNI001,2,TRUE,freesurfer,6.0.1,2022-05-24 13:46,SUCCESS
+sub-MNI001,MNI001,3,TRUE,freesurfer,6.0.1,UNAVAILABLE,INCOMPLETE
diff --git a/proj-nipoppy/derivatives/fmriprep-20.2.7/.fill b/proj-nipoppy/derivatives/fmriprep-20.2.7/.fill
diff --git a/proj-nipoppy/derivatives/fmriprep-23.1.3/.fill b/proj-nipoppy/derivatives/fmriprep-23.1.3/.fill
diff --git a/proj-nipoppy/derivatives/mriqc-23.1.0/.fill b/proj-nipoppy/derivatives/mriqc-23.1.0/.fill
diff --git a/proj-nipoppy/derivatives/neurobagel-0.0.1/.fill b/proj-nipoppy/derivatives/neurobagel-0.0.1/.fill
diff --git a/proj-nipoppy/sourcedata/dicoms/.fill b/proj-nipoppy/sourcedata/dicoms/.fill
diff --git a/proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill b/proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill
diff --git a/proj-nipoppy/sourcedata/tabular/assesments/.fill b/proj-nipoppy/sourcedata/tabular/assesments/.fill
diff --git a/proj-nipoppy/sourcedata/tabular/bagel.csv b/proj-nipoppy/sourcedata/tabular/bagel.csv
@@ -0,0 +1,3 @@
+bids_id,participant_id,session,assessment_name,assessment_score
+sub-MNI001,MNI001,1,group,Patient
+sub-MNI001,MNI001,2,group,Patient
diff --git a/proj-nipoppy/sourcedata/tabular/demographics/.fill b/proj-nipoppy/sourcedata/tabular/demographics/.fill
diff --git a/proj-nipoppy/sourcedata/tabular/manifest.csv b/proj-nipoppy/sourcedata/tabular/manifest.csv
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,4 @@
		0.0.1 2024-06-20

		- Started to work on this support of the DatasetType project