External Email - Use Caution 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. > >
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