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 <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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: <577ff153.1080...@nmr.mgh.harvard.edu
<mailto:577ff153.1080...@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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://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.
