Hi:
I am doing the freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/ fswiki/FsFastTutorial), but got an error while running the Random Effects Surface-based Group Analysis section.
The command line was:
mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii --glmdir lh.rfx.osgm --nii --surf fsaverage lh
and this is the terminal output:
Reading source surface /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial//fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial//fsaverage/surf/ lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0 cmdline mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii -- glmdir lh.rfx.osgm --nii --surf fsaverage lh sysname Darwin hostname cerezo.cis.atr.jp machine Power Macintosh user eiji FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0/lh.ces.nii logyflag 0 usedti 0 mask ../lh.mask.nii maskinv 0 glmdir lh.rfx.osgm DoFFx 0 Creating output directory lh.rfx.osgm Loading y from /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: Read 819210, expected 41943552 niiRead(): error reading from /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group- analysis-tut/sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: loading y /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii
I am not quite sure what is in 'lh.ces.nii' - from the file's time stamp it looks like it was not generated during the tutorial (Jun 19 2007).
Any help or comment will be very helpful - I am basically clueless... Thanks a lot in advance!!!
Eiji (below is the summary of my environment and problem)
--
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5
Kernel info: Darwin 8.11.0 Power Macintosh (Mac OS 10.4.11 on a G5)
SUBJECTS_DIR: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/
which mri_glmfit: /Applications/freesurfer/bin/mri_glmfit
pwd: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0
command line: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0
error message: ERROR: Read 819210, expected 41943552