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 <gr...@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 < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<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 >> <mailto:gr...@nmr.mgh.harvard.**edu<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> >> >> <http://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> >> >> <http://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. >> >> >> > -- > 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> > >
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