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 _______________________________________________ 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.
