Re: [Freesurfer] question retinotopic mapping

2012-12-13 Thread Douglas N Greve
Hi Julia, I don't think it looks terrible (unfortunately:). You might try increasing the smoothing level (maybe 10 fwhm). doug On 12/12/2012 08:02 AM, Julia Foecker wrote: Hey Doug, thanks for your reply. I tried now the polar angle mapping for the left hemisphere and I got the figure

Re: [Freesurfer] question retinotopic mapping

2012-12-10 Thread Douglas N Greve
Hi Julia, that command is fine. It will not use the fieldsign or eccen. doug On 12/10/2012 10:17 AM, Julia Foecker wrote: Dear Doug, I tried version 5 with the commands suggested on the webside and this is working

Re: [Freesurfer] question retinotopic mapping

2012-12-06 Thread Douglas N Greve
Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: thanks. attached the info file. When I

Re: [Freesurfer] question retinotopic mapping

2012-12-06 Thread Douglas N Greve
The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat

Re: [Freesurfer] question retinotopic mapping

2012-12-05 Thread Douglas N Greve
Hi Julia, what is your command line when you give it the hemisphere? Also, when you run it, put -debug as the first argument and send me the terminal output. doug On 12/05/2012 10:55 AM, Julia Foecker wrote: Hi Doug, I tried now several things to use the tksurfer command but it does not

Re: [Freesurfer] question retinotopic mapping

2012-12-05 Thread Douglas N Greve
It should automatically detect that this was a retinotopy analysis and then load the polar and eccen. Was this configured as a retinotopy analysis? Can you send me the $ANALYSIS_PHASE/analysis.info file? doug On 12/05/2012 04:12 PM, Julia Foecker wrote: Hi Doug, I tried now several ways

Re: [Freesurfer] question retinotopic mapping

2012-12-04 Thread Douglas N Greve
Hi Julia, I meant tksurfer-sess (not surf-sess) doug On 12/04/2012 05:39 AM, Julia Foecker wrote: Hi Doug, thanks for your reply. I got the following messages when running the surf-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE -retinotopy polar and there was also