HI all, I have another problem with mri_glmfit-sim. It looks for something that is not available in my FS (see below the error message) How can I solve this problem? thank you! Angela
mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat SURFACE: fsaverage lh log file is qdec/Untitled/cache.mri_glmfit-sim.log
cd /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon Sep 1 12:00:58 CEST 2014 Darwin MacBook-Pro-di-Angela-Favaro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 angelafavaro setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 37.845465 ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm38/abs/th13/mc-z.csd
I think this has something to do with the unix LOCALE because it is interpreting the "2.0" as "2,0" using the comma "," instead of the "." I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try setenv LANG en_US.UTF-8
Then run mri_glmfit-sim
doug
On 8/24/14 1:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
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