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.anderso@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

External Email - Use Caution

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.anderso@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 fischl@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.anderso@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

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:

...

External Email - Use Caution

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.anderso@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 fischl@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.anderso@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

You are going about it in the right way. Not sure about a better template. You could create the surfaces on an individual and then apply a linear transform to get it into fsaverage space. Again, another hack ...

On 1/22/19 1:56 PM, john Anderson wrote:

     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/FsFastGroupLeve...

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.anderso@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.anderso@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 fischl@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.anderso@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