External Email - Use Caution Thanks so much Ruopeng
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 Thu, Jul 5, 2018 at 1:40 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> wrote: > 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 > skype: srishti.goel12 > > > On Mon, Jun 11, 2018 at 10:34 AM, Ruopeng Wang <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 >> >> Best, >> Ruopeng >> >> >> On Jun 9, 2018, at 11:04 AM, srishti goel <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 >> skype: srishti.goel12 >> >> >> On Tue, May 29, 2018 at 2:40 PM, srishti goel <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 >>> skype: srishti.goel12 >>> >>> >>> On Tue, May 29, 2018 at 10:40 AM, Ruopeng Wang < >>> 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 >>>> 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. >>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >> >> > _______________________________________________ > 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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