FL-ready dataset

Record start time

brainflex record fl_ready_data start

Pipeline installation

Install the Nipoppy-to-Fed-BioMed conversion pipeline:

nipoppy pipeline install 23753437 --study nipoppy_study

The pipeline should now be listed when you run:

nipoppy pipeline list --study nipoppy_study

Output

WARNING  No available bidsification pipelines
INFO     Available processing pipelines and versions
INFO             - freesurfer        (7.3.2)
INFO             - nipoppy2fedbiomed (0.1.0)
INFO     Available extraction pipelines and versions
INFO             - fs_stats (0.3.0)

Dataset extraction

Combine the FreeSurfer IDPs and harmonized phenotypic data into a Fed-BioMed dataset:

nipoppy process --pipeline nipoppy2fedbiomed --pipeline-step age --study nipoppy_study
nipoppy process --pipeline nipoppy2fedbiomed --pipeline-step sex --study nipoppy_study

For each of the prediction tasks (brain age regression and biological sex classification), this will write a CSV file (the Fed-BioMed dataset) and a JSON file used to register it on the Fed-BioMed node.

tree nipoppy_study/derivatives/nipoppy2fedbiomed

Output

nipoppy_study/derivatives/nipoppy2fedbiomed
└── 0.1.0
    └── output
        ├── age
        │   ├── dataset.csv
        │   └── dataset_info.json
        └── sex
            ├── dataset.csv
            └── dataset_info.json

Record end time and answer questions

brainflex record fl_ready_data end