Dave,

I'm not 100% certain, but I think you need to create a mask volume from your subcortical.label file, and then use the --mask option with mri_glmfit instead of --label (see mri_glmfit --help). That is, create a volume with a '1' in the voxels of interest, and '0' elsewhere and pass that to --mask.

Nick

On Mon, 2009-04-20 at 13:40 -0400, Dave Brohawn wrote:

Hello,

Here is my bugr information.

FREESURFER_HOME: /usr/local/freesurfer/stable4

Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090416

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

I am curious if it is possible to run a monte carlo analysis using volume data including a label file I generated.

Here is the command I tried to run:

mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --C $SUBJECTS_DIR/fsgd/All-18.mat --label $SUBJECTS_DIR/fsaverage/label/subcortical.label --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/All18Vol_MCSIM1 --fwhm 13.37

This would be the first of ten monte carlo simulation commands. It returned an error message saying:

gdfReadHeader: reading /autofs/space/ventzl_016/users//fsgd/All-18.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 CC 2 T INFO: gd2mtx_method is dods simbase /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/All18Vol_MCSIM1 ERROR: need --surf with --label

The subcortical label I generated from the "aseg" segmentation overlay for fsaverage includes the left and right segmentations of the following regions:

Amygdala, hippocampus, DC, Putamen, Accumbens, Pallidum, Thalamus Proper, and Caudate. The brain stem label is also included.

Please let me know if running a monte carlo for volume with a label is possible.

Thank you,

Dave Brohawn _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer