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 > <gr...@nmr.mgh.harvard.edu <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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 > > 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 > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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> > <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> > > > > > 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. > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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> > >
-- 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
