Matlab FSL wrappers

This page contains links to several Matlab scripts I have written which format and call FSL commands. Many of these scripts are contained here.
The actual FSL commands only encompass a few lines of code. The bulk of the code maintains the necessary infrastructure for looping over subjects and runs within subjects.

prep_bs.m
- This script formats calls for doing the following things:
  - creating a 4D NiFTI file using avwmerge. Search for CREATE_RAW_4D.
  - extracting the brain using betfunc. Search for EXTRACT_BRAIN.
  - EPI motion correction using mcflirt. Search for MOTION_CORRECT.
  - Estimation and saving of coregistration parameters using flirt. Search for COREGISTER. This process relies on other component steps which use FSL routines, including,
    - extracting a reference volume (time point) using avwroi
  - Checking of coregistration and generation of a web-page with graphics showing the coregistration results. Search for CHECK_ALL_COREG.
  - Prepares regressors for extra physiological variables (heart rate, respiration) and calls generate_physio_evs.m to format them appropriately for FEAT.
check_coreg.m
- This script formats calls for doing the following things
  - reslices a target volume using a previously computed spatial transformation matrix using flirt.
  - generates a figure using the slicer and convert commands.
generate_physio_evs.m
set_fsf_defaults.m
- create_fsf.m ** This generates a structure populated with default values which mirrors that established by FEAT.
remove_physio.m
- This script is used for removing variance in the BOLD signal that is modeled by the heart rate and respiration recordings.
write_fsf.m ** Write a .fsf file that can be fed to FEAT.

Last updated: February 22, 2006 15:40 , Petr Janata