Research Overview
MCFLIRT is an intramodal motion correction tool designed for use on fMRI time series and based on optimization and registration techniques used in FLIRT, a fully automated robust and accurate tool for linear (affine) inter and intermodal brain image registration.
If you use MCFLIRT in your research, please quote the journal reference:
Jenkinson, M., Bannister, P., Brady, J. M. and Smith, S. M. Improved Optimisation for the Robust and Accurate Linear Registration and Motion Correction of Brain Images. NeuroImage, 17(2), 825841, 2002.
How it works
MCFLIRT loads the timeseries in its entirity and will default to the middle volume as an initial template image. A coarse 8mm search for the motion parameters is then carried out using the cost function specified followed by two subsequent searches at 4mm using increasingly tighter tolerances. All optimizations use trilinear interpolation.
As part of the initial 8mm search, an identity transformation is assumed between the middle volume and the adjacent volume. The transformation found in this first search is then used as the estimate for the transformation between the middle volume and the volume beyond the adjacent one. This scheme should lead to much faster optimization and greater accuracy for the majority of studies where subject motion is minimal. In the pathalogical cases, this scheme does not penalise the quality of the final correction.
If mean registration is used, the curent motion correction parameters are applied to the timeseries, the volumes are averaged to create a new template image and the same 3stage correction is carried out using this new mean image as a template.
Finally, if a 4stage correction has been specified, a further optimization pass is carried out using sinc interpolation (internally) for greater accuracy. This step is significantly more timeconsuming than the previous part of the correction, which should take in the order of 10 minutes for a 100 volume timeseries. This internal interpolation is independent of the final resampling interpolation (as specified by sinc_final or spline_final).
The scheme has the added advantage of `sensible' handling of the end slices in a volume. In other schemes, voxels which move out of the Field of View (FOV) due to (often slight) movement of the head are either excluded from further calculations or treated as zerovalue. In order to retain as much useful information in the data as possible, the volumes are padded by doubling the first and last slices in the zplane so that we can interpolate from locations outside the FOV using appropriate values.
Usage and options
mcflirt in <infile> [options]
Available options are:
out, o 

default is infile_mcf 
cost 

{mutualinfo,woods,corratio,normcorr,normmi,leastsquares} : default is normcorr 
bins 

default is 256 
dof 

default is 6 
refvol 

default is middle volume 
scaling 

default is 6.0 
smooth 

default is 1.0  controls smoothing in cost function 
rotation 

specify scaling factor for rotation optimization tolerances 
verbose 

0 is least and default 
stages 

default is 3. 4 specifies final (internal) sinc interpolation 
init 

initial transform matrix to apply to all vols 
gdt 

run search on gradient images 
edge 

run search on contour images 
meanvol 

register timeseries to mean volume (overrides refvol option) 
stats 

produce variance and std. dev. images 
sinc_final 

applies final transformations (resampling) using sinc interpolation 
spline_final 

applies final transformations (resampling) using spline interpolation 
mats 

save transformation matrices in subdirectory outfilename.mat 
plots 

save transformation parameters in file outputfilename.par 
report 

report progress to screen 
help 

print this information 
Output file formats
When run with the mats option, MCFLIRT saves a FLIRTcompatible transformation matrix for every 3D volume in the input image.
When run with the plots option, MCFLIRT saves a .par file, which is a plaintext file that contains the estimated rotations and translations for each 3D volume. The first three columns contain the rotations for the X, Y, and Z voxel axes, in radians. The remaining three columns contain the estimated X, Y, and Z translations. These translation parameters are defined in the scaled mm coordinate system used by FLIRT, and have been rotated by the rotation parameters with respect to the centreofmass of the reference image volume (which can be calculated with the fslstats C option, multiplying the results by the image pixdims).
General Advice
 For rapid registration, highquality corrections can be performed using only 3stage optimization with the mean template