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/FsFastFunctionalConnectivityWalkthrough > ), > 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” > > > 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > 2) Platform: OSX Yousemite > > 3) 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 > > 4) 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
