Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n - Freesurfer

9 Jul 2016

      what do you mean nothing happens? After you hit the return key, it 
should either give you the path to the command or it should say Command 
not found.
doug
ps. Please remember to post to the list and not to us individually
On 7/8/16 7:16 PM, Erik Jahner wrote:
...
When I type "which matlab” in the command window, nothing happens. My 
$PATH structure is a s follows:
echo $PATH
/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Sorry if my response seems naïve, I’am new to running command 
lines although I’m trying learn.
Erik
Message: 6
Date: Fri, 8 Jul 2016 14:30:43 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu 
mailto:greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3()
failed\n
To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <577FF153.1080602@nmr.mgh.harvard.edu 
mailto:577FF153.1080602@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
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