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Cohort creator#

TL;DR

Creates a neuroimaging cohort by aggregating data across datasets.

Install a set of datalad datasets from openneuro and get the data for a set of participants. Then copy the data to a new directory structure to create a “cohort”.

Takes 2 files as input that should list:

  • source datasets

  • subject in each dataset to be included in the cohort

For examples of 2 inputs TSV files see this page

Requirements#

Operating system#

It is recommended to use this package on a linux / Mac OS.

If you are on Windows, try using WSL (Windows Subsystem for Linux) to run this package: windows does not handle symbolic links well, and this package relies on symlinks. If you decided to go ahead anyway make sure you have got a LOT of disk space available.

More information here

Python dependencies#

Make sure you have the following installed:

  • datalad and its dependencies:

    • if you are have anaconda / conda, it should be ‘just’ a matter of running

      conda install -c conda-forge datalad

    • But check the installation instructions for more details.

Other dependencies are listed in the pyproject.toml file.

Installation#

git clone https://github.com/neurodatascience/cohort_creator.git
cd cohort_creator
pip install .

Limitations#

Latest datasets#

Currently this should allow you to access:

Number of datasets: 863 with 37441 subjects including:

  • 692 datasets with MRI data

  • with participants.tsv: 487

  • with phenotype directory: 22

  • with fmriprep: 90 (3937 subjects)

    • with participants.tsv: 74

    • with phenotype directory: 3

  • with freesurfer: 36 (3322 subjects)

    • with participants.tsv: 34

    • with phenotype directory: 2

  • with mriqc: 330 (14607 subjects)

    • with participants.tsv: 248

    • with phenotype directory: 18

It may be that very recent datasets are not available yet.

Datatypes, suffixes, Freesurfer#

Only anat | T1w and func | bold data is supported at the moment.

Not yet possible to get freesurfer data via the cohort creator, though the data is available in the sourcedata folder of the fmriprep datasets.

Blind spots#

It may be possible that that some metadata files (JSON, TSV) are not accessed over correctly if they are not in the root of the dataset or the same folder as the data file.

FIX use pybids / ancpbids for data indexing and querying.

Demo#

To get from openneuro-derivatives for all T1w

  • the MRIQC output for each file

  • the corresponding T1W file

run the following command from within the cohort_creator folder:

cohort_creator install \
  --datasets_listing inputs/datasets_with_mriqc.tsv \
  --participants_listing inputs/participants_with_mriqc.tsv \
  --output_dir outputs \
  --dataset_types raw mriqc \
  --verbosity 3

cohort_creator get \
  --datasets_listing inputs/datasets_with_mriqc.tsv \
  --participants_listing inputs/participants_with_mriqc.tsv \
  --output_dir outputs \
  --dataset_types raw mriqc \
  --verbosity 3

cohort_creator copy \
  --datasets_listing inputs/datasets_with_mriqc.tsv \
  --participants_listing inputs/participants_with_mriqc.tsv \
  --output_dir outputs \
  --dataset_types raw mriqc \
  --verbosity 3