Name: BROCCOLI
Owner: BIDS Apps
Description: BIDS App for BROCCOLI
Created: 2016-08-04 00:47:13.0
Updated: 2017-03-23 08:39:41.0
Pushed: 2017-03-23 14:02:51.0
Size: 33
Language: null
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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.
Please read the official BROCCOLI documentation
Experiencing problems? Please open an issue
When using this pipeline, please acknowledge us by citing
Command-line usage of the processing script broccolipipeline.sh is as follows:
./broccolipipeline.sh bids_dir output_dir analysis_level
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
cker pull bids/broccoli:v1.0.0
To run a first level analysis of all subjects in a BIDS dataset, run
cker 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
cker 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
cker run -i --rm \
-v /Users/yourname/data/ds005:/bids_dataset \
-v /Users/yourname/outputs:/outputs \
bids/broccoli:v1.0.0 \
/bids_dataset /outputs group
This BIDS App is using FSL. If you are considering commercial use of this App please consult the relevant licenses.