Hello,
Here is my bugr info if you need it:
FREESURFER_HOME: /usr/local/freesurfer/stable4
Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090428
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/All-18/newEMerror-tpx/ASevASc_6s
ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd $SUBJECTS_DIR
I have made a mask version of subcortical regions using mri_binarize:
mri_binarize --i aseg.mgz --match 16 --match 10 --match 49 --match 13 --match 52 --match 12 --match 51 --match 11 --match 50 --match 18 --match 54 --match 17 --match 53 --match 26 --match 58 --match 28 --match 60 --o Subcortical.nii
I am able to load this file into tkmedit over fsaverage and I see that it has all the structures I want to use as a mask for my volume-based monte carlo command. I tried running my monte carlo command as follows:
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 --mask $SUBJECTS_DIR/fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37
It looks like it wants to work, but will say:
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/SubCortVol_MCSIM1
$Id: mri_glmfit.c,v 1.138.2.9 2009/01/17 02:08:58 greve Exp $ cwd /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s cmdline mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd /autofs/space/ventzl_016/users//fsgd/All-18.fsgd --C /autofs/space/ventzl_016/users//fsgd/All-18.mat --mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37 sysname Linux hostname seymour machine i686 user jroffman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.370000 OneSampleGroupMean 0 y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii logyflag 0 usedti 0 FSGD /autofs/space/ventzl_016/users//fsgd/All-18.fsgd mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii maskinv 0 glmdir (null) IllCondOK 0 DoFFx 0 Loading y from /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii INFO: gd2mtx_method is dods Matrix condition is 1 ERROR: dimension mismatch 1 between y and mask
Do you have any ideas about how to fix this? I am not sure how to look at the matrix dimension mismatches, nor am I sure how to alter the mask I made to fit the dimensions of the ces.nii file for the analysis.
Please let me know.
Thanks!
Dave