Re: [Freesurfer] retinotopy analysis viewing in Freesurfer 5

freesurfer/fstast/bin is fine

Maryam Vaziri Pashkam wrote:

Sorry Doug this is a very basic question, Should I put the rtview file in the freesurfer/fstast/bin directory or somewhere else?

Thanks, Maryam

On Thu, Feb 16, 2012 at 3:57 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
    <mailto: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>
    <mailto:greve@nmr.mgh.harvard.edu
    <mailto:greve@nmr.mgh.harvard.edu>>

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel: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>