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
selxavg3-sess log file /Applications/freesurfer/fsfast/bin/selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh $Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $ uid=0(root) gid=0(wheel) groups=0(wheel),701(com.apple.sharepoint.group.1),1(daemon),2(kmem),3(sys),4(tty),5(operator),8(procview),9(procmod),12(everyone),20(staff),29(certusers),61(localaccounts),80(admin),702(com.apple.sharepoint.group.2),33(_appstore),98(_lpadmin),100(_lpoperator),204(_developer),395(com.apple.access_ftp),101(com.apple.access_screensharing-disabled),399(com.apple.access_ssh) /Applications/freesurfer/LagStructure 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 Mon Jul 4 11:01:40 PDT 2016 preproc-sess -s subj439rest -d /Applications/freesurfer/LagStructure -a fc.lpccseed.surf.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ root setenv FREESURFER_HOME /Applications/freesurfer setenv SUBJECTS_DIR /Applications/freesurfer/subjects 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 /Applications/freesurfer/LagStructure /Applications/freesurfer/fsfast/bin/preproc-sess -s subj439rest -d /Applications/freesurfer/LagStructure -a fc.lpccseed.surf.lh -nolog Mon Jul 4 11:01:40 PDT 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain subj439rest Template ----------------------------- mktemplate-sess -s subj439rest -d /Applications/freesurfer/LagStructure -fsd rest -nolog -update Session: /Applications/freesurfer/LagStructure/subj439rest ---------------- Mon Jul 4 11:01:40 PDT 2016 Detected input format at nii.gz subj439rest Update not needed Run: 007 ---------------- Mon Jul 4 11:01:40 PDT 2016 subj439rest 007 Update not needed Mon Jul 4 11:01:40 PDT 2016 mktemplate-sess completed subj439rest Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd rest -s subj439rest -d /Applications/freesurfer/LagStructure -nolog -update ------------------------------------------------ /Applications/freesurfer/LagStructure/subj439rest Mon Jul 4 11:01:41 PDT 2016 subj439rest Update not needed for session-level mask subj439rest Update not needed for run 007 mask subj439rest Update not needed for run 007 meanval Mon Jul 4 11:01:41 PDT 2016 mkbrainmask-sess done subj439rest Registration ----------------------------- register-sess -s subj439rest -d /Applications/freesurfer/LagStructure -fsd rest -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Mon Jul 4 11:01:41 PDT 2016
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
cd /Applications/freesurfer/LagStructure
/Applications/freesurfer/fsfast/bin/register-sess -s subj439rest -d
/Applications/freesurfer/LagStructure -fsd rest -dof 6 -per-run -nolog -update
freesurfer-Darwin-lion-stable-pub-v5.3.0
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
Session: /Applications/freesurfer/LagStructure/subj439rest ----------------
Mon Jul 4 11:01:41 PDT 2016
Run: 007 ----------------
Mon Jul 4 11:01:41 PDT 2016
Update not needed
Mon Jul 4 11:01:41 PDT 2016
register-sess completed
subj439rest MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s subj439rest -d
/Applications/freesurfer/LagStructure -fsd rest -per-run -nolog -update
Logfile is /dev/null
-------------------------------------------
/Applications/freesurfer/LagStructure/subj439rest
RunList: 007
subj439rest 007 Update not needed
Mon Jul 4 11:01:41 PDT 2016
mc-sess completed SUCCESSFULLY
subj439rest To Surface -----------------------------
rawfunc2surf-sess -fwhm 5 -s subj439rest -d
/Applications/freesurfer/LagStructure -fsd rest -hemi lh -trgsubject fsaverage
-nolog -update -per-run
instem fmcpr
outstem fmcpr.sm5.fsaverage.hemi
------------------------------
1/1 subj439rest
1/1 subj439rest 007 lh ---------
Mon Jul 4 11:01:41 PDT 2016
/Applications/freesurfer/LagStructure/subj439rest/rest/007/masks/brain.fsaverage.lh.nii.gz
does not need updating
subj439rest 007 Update not needed
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
------------------------------------------
% Mon Jul 4 11:01:41 PDT 2016
% /Applications/freesurfer/LagStructure
% fc.lpccseed.surf.lh
%--------------------------------
sxa3pwd = '/Applications/freesurfer/LagStructure'
sxa3cmd = '/Applications/freesurfer/fsfast/bin/selxavg3-sess -s subj439rest -a
fc.lpccseed.surf.lh'
which fast_selxavg3
okfile = '/tmp/selxavg3-sess-10785.ok';
if(fast_fileexists(okfile)) delete(okfile); end
monly = 0;
perrun = 0;
jkrun = 0;
DoGLMFit = 1;
DoContrasts = 1;
ConList = splitstring('L_Posteriorcingulate');
DoSynth = 0;
SynthNoiseAmp = 1;
SynthNoiseAR1 = .3;
SynthSignalAmp = 0;
SynthSeed = -1;
sess = '/Applications/freesurfer/LagStructure/subj439rest';
analysis = 'fc.lpccseed.surf.lh';
flacname = '';
outtop = '';
DoFWHM = 0;
MatlabSaveRes = 0;
SaveResUnwhitened = 0;
fast_selxavg3;
if(~fast_fileexists(okfile) && ~monly); quit; end
quit;
------------------------------------------
------------------------------------------
------- matlab output --------------------
------------------------------------------
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