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 <gr...@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<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/**FsFastIndividualRetinotopyAnal**ysis<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 > gr...@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> > > > > 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<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. > >
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