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 gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
