BIDS App for BROCCOLI
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README.md

##Description

BROCCOLI is a software for analysis of fMRI (functional magnetic resonance imaging) data and is written in OpenCL (Open Computing Language). The analysis can thereby be performed in parallel on many types of hardware, such as CPUs, Nvidia GPUs and AMD GPUs. The result is a significantly faster analysis than possible with other software packages for fMRI analysis. For example, non-linear normalization of an anatomical T1 volume to MNI space (1mm resolution) takes only 4-8 seconds with a GPU.

##Documentation

Please read the official BROCCOLI documentation

##Error reporting

Experiencing problems? Please open an issue

##Acknowledgement

When using this pipeline, please acknowledge us by citing

Eklund, A., Dufort, P., Villani, M., LaConte, S., BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs, Frontiers in Neuroinformatics, 8:24, 2014

##Usage

Command-line usage of the processing script broccolipipeline.sh is as follows:

Synopsis

./broccolipipeline.sh bids_dir output_dir analysis_level
  • bids_dir: The directory with the input dataset formatted according to the BIDS standard.
  • output_dir: The directory where the output files should be stored. If you are running group level analysis, this folder should be prepopulated with the results of the participant level analysis.
  • analysis_level: Level of the analysis that will be performed. Multiple participant level analyses can be run independently (in parallel) using the same output_dir. Options are: participant and group.

Options

Options specific to the batch processing of subject data

  • --participant_label
    The label(s) of the participant(s) that should be analyzed. The label(s) correspond(s) to sub-<participant_label> from the BIDS spec (so it does not include "sub-"). If this parameter is not provided, all subjects will be analyzed sequentially. Multiple participants can be specified with a space-separated list.

##Instructions

The bids/broccoli Docker container enables users to run fMRI analyses in parallel using OpenCL. The pipeline requires that data be organized in accordance with the BIDS specification.

To get a Docker container with BROCCOLI pre-installed, run

$ docker pull bids/broccoli:v1.0.0

To run a first level analysis of all subjects in a BIDS dataset, run

$ docker run -i --rm \
    -v /Users/yourname/data/ds005:/bids_dataset \
    -v /Users/yourname/outputs:/outputs \
    bids/broccoli:v1.0.0 \
    /bids_dataset /outputs participant 

To run a first level analysis of subject 01 only, run

$ docker run -i --rm \
    -v /Users/yourname/data/ds005:/bids_dataset \
    -v /Users/yourname/outputs:/outputs \
    bids/broccoli:v1.0.0 \
    /bids_dataset /outputs participant --participant_label 01

To run a group analysis of all subjects, run

$ docker run -i --rm \
    -v /Users/yourname/data/ds005:/bids_dataset \
    -v /Users/yourname/outputs:/outputs \
    bids/broccoli:v1.0.0 \
    /bids_dataset /outputs group

Commercial use

This BIDS App is using FSL. If you are considering commercial use of this App please consult the relevant licenses.