Hi Doug, So I did the additional smoothing and the map looks better.. It's still hard to interpret though. I was expecting alternating red and blue bands to signify V1/V2/V3 boundaries, but it's very irregular with red curves running every which way into blue splotches. Do you have any suggestions how to interpret this?
So then I just looked at the automatic parcellation of V1 and V2, which seems very different from the actual fieldsign results.. The boundaries overlap quite a bit, which seems odd. How should I treat the overlap? Thanks for your help. Michelle Alsouoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > > 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
