HI Srishti, Please download the latest build from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview <https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview> Best, Ruopeng > On Jul 11, 2018, at 3:49 PM, srishti goel <23srishtig...@gmail.com > <mailto:23srishtig...@gmail.com>> wrote: > > Hi Rupoeng, > > Yes it says built in February 2018. > > Could you please tell me once the Mac build of Freeview is updated so I can > download the newest version. > > Thank you so much, 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 Wed, Jul 11, 2018 at 3:35 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > Hi Srishti, > > The mac build of freeview on our download page appears to be quite old. If > you go to About menu, you should see the build time. We will update it > shortly. > > Best, > Ruopeng > > On 07/11/2018 03:02 PM, srishti goel wrote: >> Hi Rupoeng, >> >> I dowloaded the nightly as you had suggested, followed the steps in the link >> you had sent but I am still not able to see the z-order function. I tried it >> a couple of time, deleting and re-doing everything again but I can't see the >> z-order option in Freeview. >> >> Please let me know what else can I do to check that. >> >> 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 Wed, Jul 11, 2018 at 2:59 PM, srishti goel <23srishtig...@gmail.com >> <mailto:23srishtig...@gmail.com>> wrote: >> Hi Rupoeng, >> >> I dowloaded the nightly as you had suggested, followed the steps in the link >> you had sent but I am still not able to see the z-order function. I tried it >> a couple of time, deleting and re-doing everything again but I can't see the >> z-order option in Freeview. I have attached two screenshots of what the >> Freeview looks like to me. >> >> Please let me know what else can I do to check that. >> >> Best, >> Srishti >> <Screen Shot 2018-07-11 at 2.43.41 PM.png> >> <Screen Shot 2018-07-11 at 2.44.02 PM.png> >> >> >> 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 Thu, Jul 5, 2018 at 1:43 PM, srishti goel <23srishtig...@gmail.com >> <mailto:23srishtig...@gmail.com>> wrote: >> 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 <mailto:srish...@email.unc.edu> >> skype: srishti.goel12 >> >> >> On Thu, Jul 5, 2018 at 1:40 PM, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu >> <mailto: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 >>> <mailto: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> . 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 <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 <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
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