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
