Hi Max
we don't have a released version of a cerebellar reconstruction. We have messed around with doing so, but the issue is that the folia are *so* small, that at 1mm-ish resolution you miss a ton of them (and get topological defects, etc...).
As for the brainstem, we don't, but why would you want such a thing? Surface models are usually only useful for laminar structures.
cheers Bruce
On Sat, 2 Mar 2019, Max Crayen wrote:
External Email - Use Caution
Dear all, I ran recon-all with my dataset and I am pretty satisfied with the cortical reconstruction of both hemispheres. Unfortnuately, there was no Cerebellar reconstrucion. Is there any way to also get a surface reconstruction of the cerebellum with recon-all or is there even a seperate command for that? I tried to do it with mri_tessellate /mri/aseg.mgz 8 /lh_cerebellum.gii mri_tessellate /mri/aseg.mgz 47 /rh_cerebellum.gii and also with mri_vol2surf --mov /mri/aseg.mgz --hemi lh --surf cerebellum --mni152reg --o /lh_cerebellum.gii but both times the created .gii file seems to be empty. I read myself through many Archive threads and the freesurfer wiki, but since I am not using freesurfer regularly, I do not know what else I could do. And if a surface reconstruction is possible for the cerebellum, is it also possible for the brain stem? Thanks alot in advance! Best regards, Max Crayen
External Email - Use Caution
Hi Bruce,
we are 3D printing brains in our lab, at the moment mainly for visualization purposes. Of course, the most important parts are the cortex reconstructions of the left and right hemispheres and we are very satisfied with the results.
But we were also thinking about an entire brain model and so we looked for a way to reconstruct the cerebellum or even the brainstem.
Is there any way to create such reconstructions with freesurfer, even if they are not so detailed or show defects?
Best regards, Max
Gesendet: Sonntag, 03. März 2019 um 17:07 Uhr Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Cerebellar Cortex Reconstruction
Hi Max
we don't have a released version of a cerebellar reconstruction. We have messed around with doing so, but the issue is that the folia are *so* small, that at 1mm-ish resolution you miss a ton of them (and get topological defects, etc...).
As for the brainstem, we don't, but why would you want such a thing? Surface models are usually only useful for laminar structures.
cheers Bruce
On Sat, 2 Mar 2019, Max Crayen wrote:
External Email - Use Caution
Dear all, I ran recon-all with my dataset and I am pretty satisfied with the cortical reconstruction of both hemispheres. Unfortnuately, there was no Cerebellar reconstrucion. Is there any way to also get a surface reconstruction of the cerebellum with recon-all or is there even a seperate command for that? I tried to do it with mri_tessellate /mri/aseg.mgz 8 /lh_cerebellum.gii mri_tessellate /mri/aseg.mgz 47 /rh_cerebellum.gii and also with mri_vol2surf --mov /mri/aseg.mgz --hemi lh --surf cerebellum --mni152reg --o /lh_cerebellum.gii but both times the created .gii file seems to be empty. I read myself through many Archive threads and the freesurfer wiki, but since I am not using freesurfer regularly, I do not know what else I could do. And if a surface reconstruction is possible for the cerebellum, is it also possible for the brain stem? Thanks alot in advance! Best regards, Max Crayen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
that mri_tessellate command should have worked. It might be a gifti problem. Can you run it with our standard surface as an output and view it in freeview?
On 3/3/19 11:47 AM, Max Crayen wrote:
External Email - Use CautionHi Bruce,
we are 3D printing brains in our lab, at the moment mainly for visualization purposes. Of course, the most important parts are the cortex reconstructions of the left and right hemispheres and we are very satisfied with the results.
But we were also thinking about an entire brain model and so we looked for a way to reconstruct the cerebellum or even the brainstem.
Is there any way to create such reconstructions with freesurfer, even if they are not so detailed or show defects?
Best regards, Max
Gesendet: Sonntag, 03. März 2019 um 17:07 Uhr Von: "Bruce Fischl" fischl@nmr.mgh.harvard.edu An: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Cerebellar Cortex Reconstruction
Hi Max
we don't have a released version of a cerebellar reconstruction. We have messed around with doing so, but the issue is that the folia are *so* small, that at 1mm-ish resolution you miss a ton of them (and get topological defects, etc...).
As for the brainstem, we don't, but why would you want such a thing? Surface models are usually only useful for laminar structures.
cheers Bruce
On Sat, 2 Mar 2019, Max Crayen wrote:
External Email - Use Caution
Dear all,
I ran recon-all with my dataset and I am pretty satisfied with the cortical reconstruction of both hemispheres. Unfortnuately, there was no Cerebellar reconstrucion. Is there any way to also get a surface reconstruction of the cerebellum with recon-all or is there even a seperate command for that?
I tried to do it with mri_tessellate /mri/aseg.mgz 8 /lh_cerebellum.gii mri_tessellate /mri/aseg.mgz 47 /rh_cerebellum.gii
and also with mri_vol2surf --mov /mri/aseg.mgz --hemi lh --surf cerebellum --mni152reg --o /lh_cerebellum.gii but both times the created .gii file seems to be empty.
I read myself through many Archive threads and the freesurfer wiki, but since I am not using freesurfer regularly, I do not know what else I could do.
And if a surface reconstruction is possible for the cerebellum, is it also possible for the brain stem?
Thanks alot in advance!
Best regards, Max Crayen
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Greve, Douglas N.,Ph.D. -
Max Crayen