From 648a57de32987cea0cc1a94ca9231b49e3a2d451 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Sat, 22 Jun 2024 16:23:12 +0900 Subject: [PATCH] [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 ^^^ --- proj-nipoppy/CHANGES | 4 ++++ proj-nipoppy/README.md | 13 +++++++++++++ proj-nipoppy/code/global_config.json | 1 + proj-nipoppy/dataset_description.json | 9 +++++++++ proj-nipoppy/derivatives/bagel.csv | 4 ++++ proj-nipoppy/derivatives/fmriprep-20.2.7/.fill | 0 proj-nipoppy/derivatives/fmriprep-23.1.3/.fill | 0 proj-nipoppy/derivatives/mriqc-23.1.0/.fill | 0 proj-nipoppy/derivatives/neurobagel-0.0.1/.fill | 0 proj-nipoppy/sourcedata/dicoms/.fill | 0 proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill | 0 proj-nipoppy/sourcedata/tabular/assesments/.fill | 0 proj-nipoppy/sourcedata/tabular/bagel.csv | 3 +++ proj-nipoppy/sourcedata/tabular/demographics/.fill | 0 proj-nipoppy/sourcedata/tabular/manifest.csv | 0 15 files changed, 34 insertions(+) create mode 100644 proj-nipoppy/CHANGES create mode 100644 proj-nipoppy/README.md create mode 100644 proj-nipoppy/code/global_config.json create mode 100644 proj-nipoppy/dataset_description.json create mode 100644 proj-nipoppy/derivatives/bagel.csv create mode 100644 proj-nipoppy/derivatives/fmriprep-20.2.7/.fill create mode 100644 proj-nipoppy/derivatives/fmriprep-23.1.3/.fill create mode 100644 proj-nipoppy/derivatives/mriqc-23.1.0/.fill create mode 100644 proj-nipoppy/derivatives/neurobagel-0.0.1/.fill create mode 100644 proj-nipoppy/sourcedata/dicoms/.fill create mode 100644 proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill create mode 100644 proj-nipoppy/sourcedata/tabular/assesments/.fill create mode 100644 proj-nipoppy/sourcedata/tabular/bagel.csv create mode 100644 proj-nipoppy/sourcedata/tabular/demographics/.fill create mode 100644 proj-nipoppy/sourcedata/tabular/manifest.csv diff --git a/proj-nipoppy/CHANGES b/proj-nipoppy/CHANGES new file mode 100644 index 000000000..89d9fc1bc --- /dev/null +++ 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 new file mode 100644 index 000000000..491344fb5 --- /dev/null +++ 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 new file mode 100644 index 000000000..0967ef424 --- /dev/null +++ b/proj-nipoppy/code/global_config.json @@ -0,0 +1 @@ +{} diff --git a/proj-nipoppy/dataset_description.json b/proj-nipoppy/dataset_description.json new file mode 100644 index 000000000..599a5fd42 --- /dev/null +++ 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 new file mode 100644 index 000000000..4f4e3dfca --- /dev/null +++ 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 new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/derivatives/fmriprep-23.1.3/.fill b/proj-nipoppy/derivatives/fmriprep-23.1.3/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/derivatives/mriqc-23.1.0/.fill b/proj-nipoppy/derivatives/mriqc-23.1.0/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/derivatives/neurobagel-0.0.1/.fill b/proj-nipoppy/derivatives/neurobagel-0.0.1/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/sourcedata/dicoms/.fill b/proj-nipoppy/sourcedata/dicoms/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill b/proj-nipoppy/sourcedata/raw/sub-001/ses-A/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/sourcedata/tabular/assesments/.fill b/proj-nipoppy/sourcedata/tabular/assesments/.fill new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/sourcedata/tabular/bagel.csv b/proj-nipoppy/sourcedata/tabular/bagel.csv new file mode 100644 index 000000000..e9c85fc12 --- /dev/null +++ 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 new file mode 100644 index 000000000..e69de29bb diff --git a/proj-nipoppy/sourcedata/tabular/manifest.csv b/proj-nipoppy/sourcedata/tabular/manifest.csv new file mode 100644 index 000000000..e69de29bb