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 >> 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 > 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 > > _______________________________________________ > 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. > -- 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 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.
