Hi Julia, I don't think it looks terrible (unfortunately:). You might try increasing the smoothing level (maybe 10 fwhm). doug
On 12/12/2012 08:02 AM, Julia Foecker wrote: > Hey Doug, > > thanks for your reply. I tried now the polar angle mapping for the left > hemisphere and I got the figure attached. > > It is difficult to see the typical polar maps in that figure and I am > wondering > how to change the settings so that I will receive a typical polar angle map. > I had a 180 deg. wedge. One cycle took 38.4 sec. There were 8 cycles. The > first > 5 volumes had to be deleted. I did the follwing analysis. > > mkanalysis-sess analysis rtopy.self.lh -surface self lh -TR 1.2 -retnotopy > 38.4 > -fsd bold -fwhm 5 -paradigm rtopy.par -tpef tp-exclude.txt > > > Do you have any advices what to change so that it looks more like polar angle > maps? > > > Thanks so much for any further advices, > > best Julia > > > > > > On Mon, 10 Dec 2012 12:27:13 -0500 Douglas N Greve > <gr...@nmr.mgh.harvard.edu>wrote > >> Hi Julia, that command is fine. It will not use the fieldsign or eccen. >> doug >> >> >> On 12/10/2012 10:17 AM, Julia Foecker wrote: >>> Dear Doug, >>> >>> I tried version 5 with the commands suggested on the webside and this is >>> working >>> >>> > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) >>> . > >>> >>> However, I have only polar angle runs and I am not sure if the rtview >>> commands is only referring to polar angle maps (because the field signs are >>> included and I think that they consist of eccentricity maps as well which >>> do not have a meaning in my analysis). >>> How do I have to change the command below so that it is just referring to >>> polar maps? >>> >>> rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag >>> polar/imag.nii.gz --fsig polar/fsig.nii.gz >>> >>> >>> Many thanks for further suggestions, >>> Julia >>> >>> >>> >> -- >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
