[Freesurfer] Monte Carlos for volume data?

Hello,

Here is my bugr information, if you need.

FREESURFER_HOME: /usr/local/freesurfer/stable4

Build stamp: freesurfer-Linux-centos4-stable-v4.2.0e-20090320

RedHat release: CentOS release 5.2 (Final)

Kernel info: Linux 2.6.18-92.1.22.el5 i686

NMR Center info (/space/freesurfer exists):

machine: seymour

SUBJECTS_DIR: /autofs/space/ventzl_016/users/

PWD: /autofs/space/ventzl_016/users

ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd /autofs/space/ventzl_016/users

Can you tell me if monte carlo simulations can be used for volume data? Josh Roffman and I are curious if clusters seen in the volume will pass monte carlo simulations. I have been working closely with Kara Dyckman, and we couldn't find a precedent for monte carlos involving volume data completed in the Manoach group, a freesurfer example, or a mention of it in the archives.

I used an mgh file from the mris_preproc command below to complete monte carlos for surface data on the left hemisphere.

mris_preproc --fsgd /autofs/space/ventzl_016/users/fsgd/qdec.fsgd --target fsaverage --hemi lh --sf /autofs/space/ventzl_016/users/Subject_files/All-18 --a newEMerror-tpx --c ASevASc_6s --out /autofs/space/ventzl_016/users/All-18/preproc/lh.ASevASc.All-18.gnr.mgh

I examined a log created from this preproc command, and saw that mri_vol2surf was completed for each subject in the group, followed by a concatenate command to create the mgh file. Does this mean that the volume data is taken into account in this mgh file?

Here is one of the ten monte carlos I ran for the surface data. The other nine differ only in the MCSIM #.

mri_glmfit --y $SUBJECTS_DIR/All-18/preproc/lh.ASevASc.All-18.gnr.mgh --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --surf fsaverage lh --C $SUBJECTS_DIR/fsgd/All-18.mat --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01/lh_ASevASc_6_rfx_p05_f_MCSIM1 --fwhm 14.41

If the volume data was processed in the preproc to make the mgh file for both hemispheres, then do these monte carlos also take volume data into account? Do I run a mri_volcluster (as opposed to surfcluster) to assess volume clusters and see if they pass monte carlos with what I already have, then?

Thanks for taking the time to read this through. I know this email is on the long side.

Dave Brohawn