External Email - Use Caution Hi Dr Greve, thank you for the response... It is a genius hack ;-) Results are way much better. My objective is just to improve visualization... I would like to project statistical maps from vertex wise analysis of subcortical regions.
The same last figure in FSFAST Freesurfer WIKI https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel But instead of visualizing the merged statistical map of the three spaces on volume, I would like to project it on surface. I have results in the cerebellum and brain stem and I want to show it on surface not volume.... Also, it Would be appreciated if you provide any suggestions for a brain+cerebellum+brain stem template that can be used instead of fsaverage ... Thank you so much! John You can try mri_binarize with both --erode and --dilate (specifying the structures with --match and and output surface with --surf). Dilating then eroding might remove some of the holes (though it is a hack) On 1/22/19 10:43 AM, Bruce Fischl wrote: > Hi John > > sorry, not really. If you constrain the topology of the cerebellum you > will probably loose a lot of it since the folia are so small. You can > try using Florent Segonne's old code (mri_topologycorrection), which > will generate a discrete segmentation that has the correct topology > (hopefully!), but I don't believe that guarantees that covering the > surface of it will also be topologically correct. > > cheers > Bruce > > > On Tue, 22 Jan 2019, john Anderson wrote: ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Tuesday, January 22, 2019 7:36 AM, john Anderson <john.ande...@protonmail.com> wrote: > Hi Dr Bruce, > I applied your recommendations and I was able to create surfaces to the > cerebellum and brain stem using the command mri_tesselate. I am not happy > with the topology though... There are holes and some defects. Would you > recommend any commands to improve the topology of these structures? > Your guidance is appreciated, > John > > Sent with ProtonMail Secure Email. > > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ > On Thursday, January 10, 2019 1:37 PM, john Anderson > john.ande...@protonmail.com wrote: > > > Ah! great!! thank you so much for the great help!! > > Have a good day, > > John > > Sent with ProtonMail Secure Email. > > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ > > On Thursday, January 10, 2019 1:03 PM, Bruce Fischl > > fis...@nmr.mgh.harvard.edu wrote: > > > > > Hi John > > > we distribute an aseg.mgs with fsaverage I believe. You can just > > > tesselate that. > > > cheers > > > Bruce > > > On Thu, 10 Jan 2019, john Anderson wrote: > > > > > > > External Email - Use Caution > > > > Hi Dr Bruce, I highly appreciate your guidance. > > > > I would like to load the cerebellum and brain stem structures as an > > > > average structure similar to > > > > "fsaverage" , I usually use the command > > > > tksurferfv fsaverage lh pial -overlay <image> > > > > mri_tessellate or mri_mc would create a surface for every subject, how > > > > can I create the average of the > > > > surfaces of those structures similar to "fsaverage"? > > > > Thanks again for any highlights > > > > John > > > > Hi John > > > > you could use mri_tessellate or mri_mc to create a surface for those > > > > structures, then smooth them with > > > > mris_smooth and load them into freeview. > > > > Shouldn't be too hard. > > > > cheers > > > > Bruce > > > > On Thu, 10 Jan 2019, john Anderson > > > > wrote: > > > > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ > > > > On Thursday, January 10, 2019 7:40 AM, john Anderson > > > > john.ande...@protonmail.com wrote: > > > > > > > > Dear FS experts, > > > > > > > > > > > > For visualization purposes, is there any way to show the cerebellum and > > > > brain stem regions > > > > (similar to the attached figure), this figure was published used CONN > > > > toolbox but I am not sure > > > > how they were able to map functional data in brain surface and show the > > > > cerebellum and brain > > > > stem with fsaverage. > > > > I appreciate any suggestion > > > > Jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
