Re: [Freesurfer] Create thresholded annotations without recon-all?

/05/17 15:43, Bruce Fischl wrote: > Hi Michael > > I believe you can just run the -balabels switch, which should only take a > couple of minutes > > cheers > Bruce > On Mon, 15 May 2017, Michael Bannert wrote: > >> Dear FreeSurfer community, >> >>

[Freesurfer] Create thresholded annotations without recon-all?

Dear FreeSurfer community, I would like to perform a ROI analysis using an anatomical mask. I was thinking of using the thresholded masks in the annotations file created from running recon-all. Now I noticed that a few of my older datasets do not seem to have thresholded annotation files, but

Re: [Freesurfer] Alpha channel in color lookup tables (CLUT)

FreeSurfer version is v5.3.0 Mac OS X 10.10.5 (Yosemite) Sorry for (kind of) spamming! Have a nice weekend, Michael On 11/03/16 17:04, Michael Bannert wrote: > Dear Freesurfer community, > > I have a problem using the alpha channel in the color lookup tables. No > matter what values I

[Freesurfer] Alpha channel in color lookup tables (CLUT)

Dear Freesurfer community, I have a problem using the alpha channel in the color lookup tables. No matter what values I choose, none of them seem to affect the transparency in any way. Here is what I would like to do: I have a number of labels that I want to visualize on an inflated brain

[Freesurfer] GUI problem: Cannot open windows

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Dear Freesurfers, I have a problem with all tk* functions of FreeSurfer. It seems that whenever any of these functions try to open a window, they get stuck. Just typing tkmedit or tksurfer doesn't even show the manual entries. No error output is

Re: [Freesurfer] GUI problem: Cannot open windows

-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 Well this is a bit embarrassing: After another restart tksurfer and tkregister2 work normally. I'm a happy FreeSurfer user again. May this thread be helpful to at least one other person. Cheers, Michael On 07/05/15 11:22 , Michael Bannert wrote

Re: [Freesurfer] rtview.sh fsig

me know if you need help once you get there doug On 07/15/2013 12:31 PM, Michael Bannert wrote: Dear Freesurfer experts, I have been using Freesurfer in combination with rtview.sh to visualize my retinotopic mapping results (rotating wedge) and to define masks for individual

[Freesurfer] rtview.sh fsig

may have to discard some vertices near the fovea. -- 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] Couldn't download rtview

://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23019.html -- 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

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

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

Re: [Freesurfer] selxavg3-sess ERROR: analysis XYZ does not exist

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

[Freesurfer] Couldn't download FsFast tutorial data

Dear freesurfer community, I seem to be unable to download the FsFast tutorial data. ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData ) I tried each of the two links and I tried curl -O as well as wget but nothing worked. Any ideas? Thanks for your help! Michael -- Michael