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README.md

BARACUS: Brain-Age Regression Analysis and Computation Utility Software

CircleCI DOI

This BIDS App predicts brain age, based on data from Freesurfer 5.3. It combines data from cortical thickness, cortical surface area, and subcortical information (see Liem et al., 2017).

Requirements

Your data has to be organized according to the BIDS standard and each subject needs at least one T1w image. In a first step, BARACUS runs FreeSurfer's recon-all command and saves the output in {out_dir}/freesurfer/ If the data has previously been analyzed with FreeSurfer version 5.3.0, and BARACUS finds them in --freesurfer_dir this step ist skippen.

Important: if you use previously processed FreeSurfer data

  1. the data has to be preprocessed with Freesurfer's 5.3.0 installation, not the 5.3.0-HCP installation;
  2. FreeSurfer data needs to be BIDS-formatted, i.e. subject folders should be named sub-<subject_label>, (e.g., sub-01, sub-02...)

Also important: if you are comparing groups regarding brain-age, make sure that the groups are well matched (e.g. regarding ethnicity; see here).

Acknowledgements

If you use BARACUS in your work please cite:

  1. Liem et al. (2017),
  2. the zenodo DOI of the BARACUS version you used, and
  3. The FreeSurfer tool

Liem et al. (2017). Predicting brain-age from multimodal imaging data captures cognitive impairment. Neuroimage, 148:179–188, doi: 10.1016/j.neuroimage.2016.11.005. [preprint]

Models

Liem2016__OCI_norm: Model trained on subjects that have no objective cognitive impairment (OCI) (OCI norm in Liem et al., 2017). Sample: N = 1166, 566f/600m, age: M = 59.1, SD = 15.2, 20-80y

Liem2016__full_2samp_training: Model trained on subjects that have no objective cognitive impairment (OCI) (full LIFE 2sample training in Liem et al., 2017). Sample: N = 2377, 1133f/1244m, age: M=58.4, SD=15.4, 18-83y; containing data from the LIFE and NKI studies.

Modes

It can be run in BIDS mode (recommended) and in in FILE mode.

In BIDS mode the input is a BIDS formatted Freesurfer folder.

In FILE mode the input is provided as surface and aseg files. Surface files need to be sampled to fsaverage4 space, aseg files extracted via asegstats2table.

BIDS mode

Example

These examples demonstrate how to run the bids/baracus docker container. For a brief introduction how to run BIDS Apps see this site. In the examples /project/bids_sourcedata and /project/baracus are directories on your hard drive, which are mapped into the docker container directories /data/in and /data/out, respectively, via the -v flag.

Participants

docker run -ti --rm \
-v /project/bids_sourcedata/:/data/in \
-v /project/baracus:/data/out \
bids/baracus /data/in /data/out participant \
--license_key "XX"

Group

docker run -ti --rm \
-v /project/bids_sourcedata/:/data/in \
-v /project/baracus:/data/out \
bids/baracus /data/in /data/out group \
--license_key "XX"

Participants with previously processed FreeSurfer data

If FreeSurfer data is already available, for example at /project/freesurfer/ running the follwing command will use the previously processed data:

docker run -ti --rm \
-v /project/bids_sourcedata/:/data/in \
-v /project/freesurfer/:/data/freesurfer \
-v /project/baracus:/data/out \
bids/baracus /data/in /data/out participant \
--license_key "XX" --freesurfer_dir /data/freesurfer

Usage

usage: run_brain_age_bids.py [-h]
                             [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                             [--freesurfer_dir FREESURFER_DIR]
                             [--models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]]
                             --license_key LICENSE_KEY [--n_cpus N_CPUS] [-v]
                             bids_dir out_dir {participant,group}

BARACUS: Brain-Age Regression Analysis and Computation Utility Software. BIDS
mode. You specify a BIDS-formatted freesurfer folder as input. All data is
extracted automatiacally from that folder.

positional arguments:
  bids_dir              The directory with the input dataset formatted
                        according to the BIDS standard.
  out_dir               Results are put into {out_dir}/baracus.
  {participant,group}   Level of the analysis that will be performed.
                        "participant": predicts single subject brain age,
                        "group": collects single subject predictions.

optional arguments:
  -h, --help            show this help message and exit
  --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
                        The label of the participant that should be analyzed.
                        The label corresponds to sub-<participant_label> from
                        the BIDS spec (so it does not include "sub-"). If this
                        parameter is not provided all subjects should be
                        analyzed. Multiple participants can be specified with
                        a space separated list.
  --freesurfer_dir FREESURFER_DIR
                        Folder with FreeSurfer subjects formatted according to
                        BIDS standard. If subject's recon-all folder cannot be
                        found, recon-all will be run. If not specified
                        freesurfer data will be saved to {out_dir}/freesurfer
  --models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]
  --license_key LICENSE_KEY
                        FreeSurfer license key - letters and numbers after "*"
                        in the email you received after registration. To
                        register (for free) visit
                        https://surfer.nmr.mgh.harvard.edu/registration.html
  --n_cpus N_CPUS       Number of CPUs/cores available to use.
  -v, --version         show program's version number and exit

FILE mode

Example

docker run -ti --rm \
-v /project/data/:/data/in \
-v /project/out:/data/out \
--entrypoint=run_brain_age_files.py \
bids/baracus /data/out \
--lh_thickness_file /data/in/s01/lh.thickness.mgh \
--rh_thickness_file /data/in/s01/rh.thickness.mgh \
--lh_area_file /data/in/s01/lh.area.mgh \
--rh_area_file /data/in/s01/rh.area.mgh \
--aseg_file /data/in/s01/aseg.txt

Usage

usage: run_brain_age_files.py [-h] [--participant_label PARTICIPANT_LABEL]
                              [--models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]]
                              --lh_thickness_file LH_THICKNESS_FILE
                              --rh_thickness_file RH_THICKNESS_FILE
                              --lh_area_file LH_AREA_FILE --rh_area_file
                              RH_AREA_FILE --aseg_file ASEG_FILE
                              out_dir

BARACUS: Brain-Age Regression Analysis and Computation Utility Software. Files
mode. You specify lh/rh thickness/area + aseg file (with
--lh_thickness_file...). Surface files need to be sampled to fsaverage4 space,
aseg files extracted via asegstats2table. Only one subject can be specified at
a time.

positional arguments:
  out_dir               Results are put here.

optional arguments:
  -h, --help            show this help message and exit
  --participant_label PARTICIPANT_LABEL
                        will be written into output files and can be omitted
  --models {Liem2016__OCI_norm,Liem2016__full_2samp_training} [{Liem2016__OCI_norm,Liem2016__full_2samp_training} ...]
  --lh_thickness_file LH_THICKNESS_FILE
  --rh_thickness_file RH_THICKNESS_FILE
  --lh_area_file LH_AREA_FILE
  --rh_area_file RH_AREA_FILE
  --aseg_file ASEG_FILE