External Email - Use Caution Hi Ruopeng,
Thank you so much! That option will be super helpful. Are you planning to add that option to Freeview soon? Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > Hi Srishti, > > In freeview surface labels are always displayed on top of overlays. I will > add an option to change that. > > Best, > Ruopeng > > > On May 28, 2018, at 9:18 AM, srishti goel <23srishtig...@gmail.com> wrote: > > Hello, > > I did use Freeview but I think using either TkSurfer or Freeview won't > matter because what I am trying to figure out is what the fthresh value > means for the map. > From reading the archive, I understand that, for instance, fthresh value > of 0.3 will mean that the overlay displays 50% (1/10^3) threshold based on > intensity/ only voxels which are overlaid by 50% of the subjects. In my > case, the maps are visible at fthresh 0.1 and below but since these are > already thresholded maps from a meta-analysis I am not very clear on how to > interpret the fthresh here. Is it voxels overlaid by ~80% of studies? > > The other thing I want to figure out is that right now when I view my > overlay with two other labels, the labels (when in solid color and not > outline) cover my overlay. But I would want it the other way round such > that the overlay comes on top of the solid colored labels. Does anyone know > how I can achieve that? > > Thank you so much! > > Best, > Srishti > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Fri, May 25, 2018 at 10:09 AM, Douglas Greve <dgr...@mgh.harvard.edu> > wrote: > >> I don't know anything about neuroelf, but unless your have a binarized >> map, then the map is going to change when you change the threshold. BTW, if >> you wan to use freeview, you can run tksurferfv with the same args as >> tksurfer >> >> On 5/22/18 3:49 PM, srishti goel wrote: >> >> >> Hello, >> >> I am trying to view network based maps produced from a meta-analysis >> using neuroelf on the surface in freesurfer. The meta-analytic maps are >> thresholded maps that represent the proportion of contrasts that activated >> at each voxel >> >> I projected my maps on the surface using: >> mri_vol2surf --src negative_allsocial_proportion.img --regheader >> mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac 0.5 >> Then to view it used: >> tksurfer mni152_subject lh inflated -overlay ./neg_allsocial_lh.nii >> -fthresh 0.05 >> The issue I have is with the fthresh value. I read the wiki and some >> stuff on archive about the fthresh value but I am unsure what it exactly >> means and does. My issue is that the display of my maps changes when I >> change the fthresh value even though the maps have been k-thresholded using >> neuroelf before exporting them to freesurfer. More area is marked up when I >> decrease the threshold value from 0.1 to 0.05 and nothing is visible above >> 0.1 >> >> Does anyone have any thoughts about what might be going on there and how >> I can fix it? >> Do I need to do something totally different from what I am doing? >> >> Best, >> Srishti >> Social/Clinical Research Specialist >> Child Imaging Research and Life Experiences Lab >> University of North Carolina at Chapel Hill >> email (W): srish...@email.unc.edu >> skype: srishti.goel12 >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > >
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