FreeSurfer IDPs

Install pipelines

Install the FreeSurfer and FreeSurfer stats extraction pipelines:

# FreeSurfer
nipoppy pipeline install 21929473 --study nipoppy_study

# fs_stats
nipoppy pipeline install 23752946 --study nipoppy_study

Note

The --study option is not needed if your working directory is somewhere inside nipoppy_study.

Confirm that the pipeline have been installed correctly:

nipoppy pipeline list --study nipoppy_study

Output

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

Configure the fs_stats pipeline with your FreeSurfer license

The fs_stats pipeline requires a FreeSurfer license because it runs lightweight tools that are packaged with FreeSurfer. Open the study configuration file at nipoppy_study/global_config.json and set FREESURFER_LICENSE_FILE to the absolute path to your FreeSurfer license. FreeSurfer licenses can be obtained by filling out this form.

    "PIPELINE_VARIABLES": {
        "BIDSIFICATION": {},
        "PROCESSING": {},
        "EXTRACTION": {
            "fs_stats": {
                "0.3.0": {
                    "FREESURFER_LICENSE_FILE": null
                }
            }
        }
    },

Extract FreeSurfer statistics

nipoppy extract --pipeline fs_stats --study nipoppy_study

This will print a lot of output, with the final lines being this:

Output

INFO     [RUN STDOUT] Exit code
INFO     [RUN STDOUT] 0
INFO     [RUN STDOUT] Error message
INFO     [RUN STDOUT]
INFO     [RUN STDOUT] Output files
INFO     [RUN STDOUT]
INFO     [RUN STDOUT] Missing files
INFO     [RUN STDOUT]
INFO     [RUN STDOUT]
INFO     Ran on the entire study 🎉🎉🎉

The pipeline writes a set of files to nipoppy_study/derivatives/freesurfer/7.3.2/idp.

tree nipoppy_study/derivatives/freesurfer/7.3.2/idp

Output

nipoppy_study/derivatives/freesurfer/7.3.2/idp
└── fs_stats-0.3.0
    ├── fs7.3.2-aparc.a2009s-area.tsv
    ├── fs7.3.2-aparc.a2009s-meancurv.tsv
    ├── fs7.3.2-aparc.a2009s-thickness.tsv
    ├── fs7.3.2-aparc-area.tsv
    ├── fs7.3.2-aparc.DKTatlas-area.tsv
    ├── fs7.3.2-aparc.DKTatlas-meancurv.tsv
    ├── fs7.3.2-aparc.DKTatlas-thickness.tsv
    ├── fs7.3.2-aparc-meancurv.tsv
    ├── fs7.3.2-aparc-thickness.tsv
    └── fs7.3.2-aseg-volume.tsv