Is matlab in your path? What happens if you type which matlab at the command line?
On 07/08/2016 12:34 AM, ERIK JAHNER wrote:
Hello FreeSurfer Developers,
This is Erik Jahner, I’m attempting to complete the final step in the tutorial concerning FSFast Functional connectivity walkthrough (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr... ), but for I get the following error when I run the following command:
selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh
Mon Jul 4 11:01:41 PDT 2016
rawfunc2surf-sess completed
Started at Mon Jul 4 11:01:40 PDT 2016
Ended at Mon Jul 4 11:01:41 PDT 2016
preproc-sess done
/Applications/freesurfer/LagStructure/subj439rest
Mon Jul 4 11:01:41 PDT 2016
anadir = /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------- matlab output --------------------
matlab: Command not found.
*ERROR: fast_selxavg3() failed\n*
I've searched the list and no similar errors have been reported. I have tried to reinstall MATLAB; I have tried following the instructions to install the runtime environment; I have tried redoing all analysis from scratch. I have noticed that STEP 5 does not work unless I change the -cfg from “L_Posteriorcingulate.config” to “mean.L_Posteriorcingulate.config”. I don’t think this is the problem, but I thought I would point it out.
My session directory is “subj439rest”
Instead of titling the sub directory “bold”, I titled it “rest”
FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
Platform: OSX Yousemite
uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version
15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
- selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached
Here are the command lines I put in for steps 4-8, incase this is of some use:
STEP 4
fcseed-config-segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest -mean-cfg mean.L_Posteriorcingulate.config
STEP 5
fcseed-sess-s subj439rest -cfg mean.L_Posteriorcingulate.config
STEP 6
fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
fcseed-sess -s subj439rest -cfg wm.config
fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config
fcseed-sess -s subj439rest -cfg vcsf.config
STEP7
mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run
STEP 8
selxavg3-sess-s subj439rest -a fc.lpccseed.surf.lh
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