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:
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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
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‐‐‐‐‐‐‐ 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
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‐‐‐‐‐‐‐ 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
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