After you load the label or overlay you should see it on the left panel. Best, Ruopeng
> On Jul 5, 2018, at 12:54 PM, srishti goel <23srishtig...@gmail.com> wrote: > > External Email - Use Caution > > > Hi Rupoeng, > > We downloaded the nightly build for that option but I don't see it coming on > the GUI. I scrolled through every option on the task bar and also the left > panel on the GUI but nothing corresponded to 'z-order'. Could you please > direct me to where exactly should I be looking for this option? > > Thanks, > 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 <mailto:srish...@email.unc.edu> > skype: srishti.goel12 > > > On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > Yes, I have put an option called z-order in the GUI to control order of > rendering for overlays, labels and annoations. To use it you will need to > download and install the nightly build from here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview > <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview> > > Best, > Ruopeng > > >> On Jun 9, 2018, at 11:04 AM, srishti goel <23srishtig...@gmail.com >> <mailto:23srishtig...@gmail.com>> wrote: >> >> External Email - Use Caution >> >> >> Hi Ruopeng, >> >> I just wanted to check and see if there is any update about adding the >> option of changing surface labels to come below overlays in Freeview. >> Thanks! >> >> 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 <mailto:srish...@email.unc.edu> >> skype: srishti.goel12 >> >> >> On Tue, May 29, 2018 at 2:40 PM, srishti goel <23srishtig...@gmail.com >> <mailto:23srishtig...@gmail.com>> wrote: >> Thanks a lot Ruopeng, really appreciate it. >> >> 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 <mailto:srish...@email.unc.edu> >> skype: srishti.goel12 >> >> >> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu >> <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: >> It will be added very soon. I'll let you know when it is ready. >> >> Best, >> Ruopeng >> >> On 05/28/2018 05:35 PM, srishti goel wrote: >>> 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 <mailto:srish...@email.unc.edu> >>> skype: srishti.goel12 >>> >>> >>> On Mon, May 28, 2018 at 2:28 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu >>> <mailto: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 >>>> <mailto: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 <mailto:srish...@email.unc.edu> >>>> skype: srishti.goel12 >>>> >>>> >>>> On Fri, May 25, 2018 at 10:09 AM, Douglas Greve <dgr...@mgh.harvard.edu >>>> <mailto: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 <mailto:srish...@email.unc.edu> >>>>> skype: srishti.goel12 >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <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 >>>> <http://www.partners.org/complianceline> . 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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 >>> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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
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