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. >> >> >
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