Hi Alexa, you are running into problems by mixing versions. Try running both mri_glmfit and mri_glmfit-sim using 5.1 doug

ALEXA HUBER wrote:

Hi all,

I am a new freesurfer user and am trying to use mri_glmfit-sim with --cache option from my freesurfer 4.5.0 installation.

I followed the instructions on this page:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14415.html

but as the files are not available for download any more from the link indicated on that page, I instead downloaded the newest freesurfer version (v5.1.0) and took the files from there. I copied the "mult-comp-cor" directory into $FREESURFER_HOME/average/. and replaced the "mri_glmfit-sim" file in $FREESURFER_HOME/bin/. as suggested.

I then ran the simulation on a previously done glm analysis like this: mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos

The programme stops with error and gives me feedback as shown below.

Does anybody know what I did wrong? I prefer not to switch to the newest freesurfer version as I heard this is not a good idea during an analysis (is that right?). Many thanks for any help!

Alexa

Here is the feedback:

cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir

WARNING: unrecognized mri_glmfit cmd option doss

SURFACE: fsaverage lh log file is n49.lh.ZM11_2age_oldf2.thick.glmdir/cache.mri_glmfit-sim.log

cd /STORAGES/storage2/dati/FREESURFER/glm /usr/local/freesurfer-4.5.0/bin/mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos

$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Wed Nov 23 18:37:40 CET 2011 Linux fisiologia24 2.6.37.6-0.5-default #1 SMP 2011-04-25 21:48:33 +0200 x86_64 x86_64 x86_64 GNU/Linux neuroscienze setenv SUBJECTS_DIR /STORAGES/img800/home/neuroscienze/subjects FREESURFER_HOME /usr/local/freesurfer-4.5.0

Original mri_glmfit command line: cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir

DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = 14.676053 CSD /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd fname2ext: Command not found. mri_surfcluster --in n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/sig.mgh --csd /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd --mask n49.lh.ZM11_2age_oldf2.thick.glmdir/mask.mgh --cwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster. --vwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.voxel. --sum n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster.summary --ocn n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn. --oannot n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn.annot --annot aparc --csdpdf n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.pdf.dat --cwpvalthresh .05 --o n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.masked. --no-fixmni --surf white ERROR: Option --no-fixmni unknown