So when viewing with tksurfer I am assuming that -map angle shows the polar data. It looks ok. There's a lot of yellow and red, which I am assuming is the overall significance and not significance by position yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle To view eccen data, is it -map eccen? thanks. michelle Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > How do the eccen and polar look by themselves? You can look at them > with tksurfer-sess > doug > > Michelle Umali wrote: >> Hi Freesurfers, >> I'm troubleshooting my retinotopy data and am still having issues >> with wonky fieldsign data. The registration looked ok, so now I am >> trying to look at the retinotopy results using rtview. I got an >> error message saying it can't find the register.dof6.dat file. So, >> now I am stepping back to the beginning. Below are the commands I >> used for the analysis. >> >> -Does one need to specify starting position of wedge/size of wedge? >> >> Any help would be greatly appreciated. >> Michelle >> _____________ >> Here are the commands I used: >> >> recon-all -all ld09 >> >> tksurfer sj09 lh inflated and then for rh. >> Then I cut occipital patches. >> >> Then I registered the eccen and polar f.nii files: >> bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat >> tkregister2 --mov f.nii --reg register.dat --surf >> mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat >> mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy >> 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force >> mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy >> 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force >> preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force >> selxavg3-sess -a rtopy.self.lh -s sj09 >> selxavg3-sess -a rtopy.self.rh -s sj09 >> fieldsign-sess -a rtopy.self.lh -occip -s sj09 >> fieldsign-sess -a rtopy.self.rh -occip -s sj09 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > -- > 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 > > > > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
