preprocessfmri is a set of MATLAB scripts for pre-processing fMRI data (including 
slice time correction, motion correction, and spatial undistortion based on fieldmap
measurements).  It is developed by Kendrick Kay (kendrick@post.harvard.edu, 
http://kendrickkay.net).

The main novelty of the code lies in the handling of the fieldmaps (including
using local linear regression to smooth the fieldmaps and the ability to 
interpolate fieldmap measurements smoothly over time).  The code is powerful 
and has many features but may therefore be somewhat complicated to apply.

The code has several dependencies:
- SPM (for motion correction routines)
- FSL (for the "prelude" utility)
- ba_interp3 (included in the "external" folder)
- NIFTI_20110215 (included in the "external" folder)
- knkutils (see http://github.com/kendrickkay/knkutils)

Notes:
- The code is incompatible with newer versions of the NIFTI toolbox.
  Update: Actually, the code appears to be compatible with "NIfTI_20140122".
- You may have to mex ba_interp3 for your own platform (try "which ba_interp3 -all").

Contents:
- preprocessfmri.m - The main function.  Instead of calling this function directly,
                     you probably want to write a script that makes the call easier.
- preprocessfmri_standardscript.m - A template script that calls preprocessfmri.m
- preprocessfmri_CNIscript.m - A template script that calls preprocessfmri.m
- README - The file you are reading
- utilities - A directory containing various utility functions
- external - External toolboxes included for your convenience

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CHANGE HISTORY

History of major code changes:
- 2016/02/05 - cubic-interpolation case of preprocessfmri now uses padding.
- 2013/06/24 - Version 1.0.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% COPYRIGHT

Copyright (c) 2013, Kendrick Kay
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.

The name of its contributors may not be used to endorse or promote products 
derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.