
These files in this directory can be used to perform correction for
multiple comparisons on the surface on a cluster-wise or voxel-wise
basis. They are provided so that users do not have to run the
simulations themselves. 

The files are the result of Monte Carlo simulations conducted by
synthesizing white Gaussian noise on the surface, smoothing by a
certain full-width/half-max (FWHM) within the given label, rescaling,
thresholding at a certain voxel-wise threshold of a certain sign, then
recording the maximum cluster size and maximum significance value.
This constitutes an "mc-z" simulation in mri_glmfit.

These simulations were done for each hemisphere. The directories
are organized as follows:

subject/hemi/label/fwhm/sign/thresh

label is currently only cortex (?h.cortex.label). There are thirty
FWHMs ranging from 1 to 30. The signs are abs (absolute, unsigned),
pos (positive), and neg (negative). The voxel-wise thresholds are in
"significance" format (ie, -log10(p)) and are 1.3 (p<.05), 2.0 (p<.01),
2.3 (p<.005), 3.3 (p<.001), 3.3 (p<.0005), and 4.0 (p<.0001). The
actual directory for the threshold is given by "thXX" where XX is 10
times the significance level.

There is also a mask.mgh file in subject/hemi/label that indicates
the label/mask used during simulation. This must match that found in
the mri_glmfit output directory.

Each simulation was run with 10000 iterations using the following
program:

mri_mcsim --o subject/hemi/label --base mc-z \
      --surf subject hemi --nreps 10000

This will loop through all the FWHMs, signs, and thresholds in a
efficient fashion. Note, however, that this may take weeks (yes, weeks)
to complete. But it can be parallelized with something like:

foreach job (1 2 3 4)
  set cmd = (mri_mcsim --o subject/hemi/label --base mc-z.j00$job \
      --surf subject hemi --nreps 2500)
  # only save mask on 1st job
  if($job != 1) set cmd = ($cmd --no-save-mask); 
  $cmd
end

Then merge the 4 jobs into one file with:

mri_surfcluster \
   --csd-out subject/hemi/label/fwhm/sign/thresh/mc-z.csd \
   --csdpdf subject/hemi/label/fwhm/sign/thresh/mc-z.cdf \
   --csd subject/hemi/label/fwhm/sign/thresh/mc-z.j001.csd \ 
   --csd subject/hemi/label/fwhm/sign/thresh/mc-z.j002.csd \ 
   --csd subject/hemi/label/fwhm/sign/thresh/mc-z.j003.csd \ 
   --csd subject/hemi/label/fwhm/sign/thresh/mc-z.j004.csd \  
   --csdpdf-only

The "mc-z.csd" file is the file that is used to correct for multiple
comparisons in mri_surfcluster. The "CDF" is the cumulative
distribution function which describes the statistics of the simulation
results.









