Message: 6
Date: Fri, 8 Jul 2016 14:30:43 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3()
failed\n
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <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/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

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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------------------------------