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 greve@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 greve@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 greve@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 greve@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 greve@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 >>>> greve@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 >> greve@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 greve@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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 greve@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
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