yes, B is correct. The error says that it cannot find matlab. Is it in your path?
doug

On 5/25/12 9:16 AM, Michael Bannert wrote:

Hi Doug,

Thanks for your help! No, the current directory is the "Project" directory (refering to naming conventions in http://www.freesurfer.net/fswiki/FsFastTutorialV5.1/FsFastDirStruct). It is identical to $FUNCTIONALS_DIR.

The rtopy.self.lh folder is in the "Sess0x" directory and contains only the file called "analysis.info".

I actually tried two different commands:

A: selxavg-sess -s ex01s05 -a rtopy.self.lh

B: selxavg3-sess -s ex01s05 -a rtopy.self.lh

I suspect that version B is the correct one. I accidentally posted the wrong code in the previous email. Sorry! I tried both with the same negative outcome.

I now moved the rtopy.self.lh folder into the "Project" folder and tried running the command again. (I think I have to run this command from "Project" because otherwise Freesurfer tells me that it can't find the session.) That gave me the following output:

>> !selxavg3-sess -s ex01s05 -a rtopy.self.lh

Surface data self lh

--------------------------------------------------------------

selxavg3-sess logfile is /Users/mbannert/experiments/freesurfer/mc_retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120524182304.log

--------------------------------------------------------------

-------------------------------------------

/Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05 

Thu May 24 18:23:04 CEST 2012

anadir = /Users/mbannert/experiments/freesurfer/mc_retinotopy/ex01s05/bold/rtopy.self.lh

DoGLMFit = 1

DoContrasts = 1

UpdateNeeded = 1

------------------------------------------

------- matlab output --------------------

matlab: Command not found.

cat: stdout: Broken pipe

------------------------------------------

ERROR: fast_selxavg3() failed\n

Btw: I'm running all these commands from inside a Matlab shell. I hope this isn't a problem.

Thanks for your support!

Best regards,

Michael

On May 24, 2012, at 4:33 PM, Douglas N Greve wrote:

Hi Michael, is rtopy.self.lh in the current directory (the one that you
are running selxavg from)?
doug

On 05/24/2012 07:57 AM, Michael Bannert wrote:

Hi all,

I'm trying to analyze a retinotopic mapping dataset using FsFast but

some things don't seem to work the way they should.

When running "selxavg-sess -s ex01s05 -a rtopy.self.lh", I get the

following error:

"ERROR: analysis rtopy.self.lh does not exist, see mkanalysis-sess"

However, I checked that rtopy.self.lh does in fact exist. I also made

sure that the folder contains the file analysis.info

<http://analysis.info>. Why do I still get this error message?

Here is the contents of analysis.info <http://analysis.info>:

# FSBUILD freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

# MKAVERSION $Id: mkanalysis-sess,v 1.64.2.1 2011/03/22 16:58:57 greve

Exp $

# MKACMD

/Users/mbannert/../../Applications/freesurfer/fsfast/bin/mkanalysis-sess

-a rtopy.self.lh -surface self lh -TR 3.12 -retinotopy 49.92 -paradigm

rtopy.par -funcstem fmcsurfsm5 -fsd bold -nskip 0 -force

# DATE Thu May 24 11:50:39 CEST 2012

analysis rtopy.self.lh

mcstem fmcpr

funcstem fmcsurfsm5

fsd bold

TR 3.12

RegDOF 6

RawSpace surface self lh

mask brain

RawFWHM 0

RawSTC none

UseB0DC 0

inorm 100

acfbins 0

fixacf  1

acffwhm 20

acfsvd  0

designtype retinotopy

nskip 0

polyfit 2

HPFCutoffHz 0

HeteroGCor 0

parname rtopy.par

period 49.92

Any ideas? Thanks for your help!

Michael

--

Michael Bannert, Dipl.-Psych.

Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of

Tübingen & BCCN Tübingen

Otfried-Müller-Str. 25, 72076 Tübingen, Germany

Phone: +49 - (0)7071 / 29 - 89031

_______________________________________________

Freesurfer mailing list

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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--
Michael Bannert, Dipl.-Psych.

Vision & Cognition Lab, Centre for Integrative Neuroscience, Univ. of Tübingen & BCCN Tübingen

Otfried-Müller-Str. 25, 72076 Tübingen, Germany

Phone: +49 - (0)7071 / 29 - 89031

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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.