rtview will give you the colorwheel, see if that works for you
doug

Katie Bettencourt wrote:

Without the color wheel, how are you supposed to see the different meridians so that you can draw the boundaries for visual areas?  I know that field sign can do that in occipital if you have polar and eccen, but it doesn't work well with parietal retinotopy or if you don't have eccen data (which so far is not worthwhile to collect for parietal retinotopy).  What do you recommend using?  We looked at the sig maps and the angle maps per the instructions on the wiki page, but neither of them gave us the boundaries, even within occipital, and we've done this data with 4.5 and know that it comes out correctly there, so it's not an error in our data.

Katie

On Thu, Feb 16, 2012 at 3:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

   Hi Katie, the color wheel became difficult to support (and I think
   it is inferior for viewing for various reasons). There is an
   alternative called rtview. It is not in the distribution, but you
   can get it from

   ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview

   Look at the --help to see how to run it.

   doug



   Katie Bettencourt wrote:

       I have a question about the retinotopy analysis in freesurfer
       5.  I was following these instructions :
       http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis
        with some minor edits because we don't have eccen data.  And
       now I'm ready to view the data, but I'm confused by what I am
       seeing.

       I have a lot of previous retinotopy experience with older
       versions of freesurfer, and have this data all analyzed using
       Freesurfer4.5 and it works fine.  However, with Freesurfer 5
       when I use this command (with the correct sessid and
       hemisphere added in):

       tksurfer-sess -a rtopy.self.?h -s sessid

       it gives me a heat map, instead of the standard colors that
       match to the upper, lower, and horizontal meridians (i.e. red,
       green, and blue).  I also tried using the "raw angle" code:

       tksurfer-sess -a rtopy.self.?h -s sessid -map angle

       but it doesn't give me the three colors either, but a sort of
       heat like map with 2 colors, but the colors don't map to the
       different visual areas, even in occipital cortex.  Field sign
       doesn't work because I don't have the eccen data (and because
       I'm care about parietal retinotopy, not occipital).  Is there
       a way to get the standard view of retinotopy out of freesurfer 5?


       For reference in freesurfer4.5, I would load retinotopy data
       by using this command:

       tksurfer subjname ?h inflated

       and then load the map-imag-lh.w in one overlay layer, and
       map-real-lh.w in the second overlay layer, then configuring
       the overlay to display the color wheel color scale and complex
       display options, and then configuring the phase encoding
       display to 2 angle cycles and an appropriate angle offset.

       Can you help me figure out how to get my data to display
       correctly?

       Thanks,

       Katie


   --     Douglas N. Greve, Ph.D.
   MGH-NMR Center

   greve@nmr.mgh.harvard.edu <mailto:greve@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
   <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

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   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
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--
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