BFP: BrainSuite Functional Pipeline

BFP: BrainSuite fMRI Pipeline

This pipeline takes fMRI and anatomical data and processes them using a series of scripts from AFNI, BrainSuite and FSL. The functional processing script is based on batch_process.sh script from fcon1000.

System Requirements

The current version of BFP is Linux only. A Debian based Linux distribution (Ubuntu/Mint/Debian), 8GB RAM recommended. For Windows users, you can try using a virtual machine, but we have not done testing on such configurations, so we do not support it at the moment. We are currently developing a Docker-based BIDS App version of BFP, which we expect to release in late June 2018.

Installation and Setup

  • Install AFNI (Ver. Jun 12 2017 or newer) and FSL 5.0. We recommend using NeuroDebian, as it makes the installation process easier. BFP has been tested with this configuration, but it should work for other versions of Linux and other softwares. However we recommend and support the above mentioned versions.

  • Install BrainSuite 18a.

  • Install Matlab 2017a if you want to run it from Matlab
  • Download bfp, unzip
  • Open bfp.mtx in Matlab Live Notebook and edit User Inputs section.
  • open <bfpdir>/supp_data/config.ini and set paths for FSL, AFNI and BrainSuite.
  • For preprocessing fMRI, run src/preproc/bfp.mtx

Usage

Matlab

bfp(configfile,t1,fmri,studydir,subid,sessionid,TR)

configfile: Configuration file that you edited during installation, (<bfpdir>/supp_data/config.ini)

t1: T1 image in NIFTI-1 format e.g. ‘sub01-bT1w.nii.gz’

fmri: string or cell array of fMRI NIFTI-1 formatted files e.g. ‘sub_01_rest_bold.nii.gz’

studydir, subid: Outputs will be saved in the studydir/subid for each subject e.g. studydir=’mystudy’, subid=’sub-01′

sessionid: string or cell array of session id for the input fmris e.g. ‘rest’ for resting state

e.g.,
bfp /home/ajoshi/bfp/supp_data/config.ini /home/ajoshi/sub-01_T1w.nii.gz /home/ajoshi/sub-01_rest.nii.gz /home/ajoshi/mystudy sub-01 rest 2

Binary

You can run BFP from the bash shell using the command mentioned below.

bfp.sh /home/ajoshi/bfp/supp_data/config.ini /home/ajoshi/sub-01_T1w.nii.gz /home/ajoshi/sub-01_rest.nii.gz /home/ajoshi/mystudy sub-01 rest 2