Michelle Umali wrote: > Hi Doug, > I've already smoothed by 5 during preproc-sess, so does this mean I > should do additional smoothing during fieldsign-sess step? > Try the additional one now to see if it fixes the map. > Also, is this the correct command to use the sphere and not the patch: > fieldsign-sess -a rtopy.self.lh -fwhm 5 -sphere -s sj09 > yes doug > Thanks. > Michelle > > > Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > >> Try smoothing (eg, -fwhm 5) when running fieldsign-sess. You can also >> try using the sphere instead of the occip patch. >> doug >> >> Michelle Umali wrote: >> >>> Hi Doug, >>> >>> Thanks again for your advice, the heat maps look much better. However, >>> they still do not visualize the continuous range of angles or >>> eccentricities but rather divide it into two intervals such as red vs. >>> blue. Is there any way to adjust the color range to make it more >>> appropriate for this kind of data? >>> >>> The heat map for the field sign data still looks speckled. I attached >>> an image showing the heat maps for polar angle, eccentricity, and >>> field sign, with the corresponding overlay settings. >>> >>> I used 5mm smoothing. >>> >>> Thank you very much, >>> Michelle >>> >>> >>> >>> Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>> >>> >>>> The activation looks pretty reasonable. As you point out, the angles >>>> are a mess. How did you set the color scale for the angles? You should >>>> leave it as a heat scale (if you're using tksurfer-sess). How much did >>>> you smooth? >>>> >>>> doug >>>> >>>> Michelle Umali wrote: >>>> >>>>> Hi Doug, >>>>> Attached is a pic of the significance and angle maps for polar and eccen. >>>>> >>>>> What do you think? >>>>> >>>>> Thanks. >>>>> Michelle >>>>> >>>>> Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>>> >>>>> >>>>>> what does the activation look like? Does it look right? Can you >>>>>> send a pic? >>>>>> doug >>>>>> >>>>>> Michelle Umali wrote: >>>>>> >>>>>>> Hi Doug, >>>>>>> The z-values are consistently near or greater than 4. It just >>>>>>> seems that the >>>>>>> visualization of the angles is somehow incorrect... >>>>>>> >>>>>>> Is there be anything else that I need to check? >>>>>>> >>>>>>> Thanks. >>>>>>> Michelle >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> >>>> -- >>>> 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 >>>> >>> >>> >>> ----- End forwarded message ----- >>> >>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 > > >
-- 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
