You might need to smooth even more. Michelle Umali wrote: > Dear Bruce & Doug, > Thanks I'll do the label comparison. > I am attaching a fieldsign pic to show the irregularity of the > blue/red bands. Can you suggest a method of determining V1/2/3 based > on the odd pattern? > > Thank you very much. > Michelle > >>> they have to overlap unless the classification was 100% accurate >>> with no variability. You can just pick the label with the highest >>> probability at each vertex > > Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> can you send a pic? >> >> Michelle Umali wrote: >>> 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 >>> >>> >>> >> >> -- >> 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
