Hello,
I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.
Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process.
Best regards, Paula Räisänen
Helsinki University of Technology, Department of Biomedical Engineering and Computational Science
Some bumps are normal. I think you should post a screenshot.
2009/7/8, pcraisan@cc.hut.fi pcraisan@cc.hut.fi:
Hello,
I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.
Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process.
Best regards, Paula Räisänen
Helsinki University of Technology, Department of Biomedical Engineering and Computational Science
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Paula, can you send us a snapshot? The inflated surface can have bumps in it, which usually are not a problem. You can also inflate more using the -n switch. From the surf dir:
mris_inflate -n 10 lh.smoothwm lh.inflated
where 10 is the default and you can increase it to get smoother surfaces.
cheers, Bruce
On Wed, 8 Jul 2009 pcraisan@cc.hut.fi wrote:
Hello,
I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.
Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process.
Best regards, Paula Räisänen
Helsinki University of Technology, Department of Biomedical Engineering and Computational Science
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Here's the snapshot as an attachment. I would like to get rid of the bigger bumps on the front.
How do the bumps appear on the wm volume? I've used the Save point feature between tkmedit and tksurfer but I seem to be having difficulties locating the actual defect on the wm volume since I am new to freesurfer.
Cheers, Paula
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Paula, can you send us a snapshot? The inflated surface can have bumps in it, which usually are not a problem. You can also inflate more using the -n switch. From the surf dir:
mris_inflate -n 10 lh.smoothwm lh.inflated
where 10 is the default and you can increase it to get smoother surfaces.
cheers, Bruce
On Wed, 8 Jul 2009 pcraisan@cc.hut.fi wrote:
Hello,
I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.
Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process.
Best regards, Paula Räisänen
Helsinki University of Technology, Department of Biomedical Engineering and Computational Science
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Paula,
these aren't defects, they are just small scale bumps that aren't quite smoothed out. They only need manual intervention if the ?h.white and/or ?h.pial surfaces do not appear accurate in tkmedit. I think the ones you are showing are fine, but double check the surfaces to make sure.
cheers, Bruce
On Wed, 8 Jul 2009 pcraisan@cc.hut.fi wrote:
Hi,
Here's the snapshot as an attachment. I would like to get rid of the bigger bumps on the front.
How do the bumps appear on the wm volume? I've used the Save point feature between tkmedit and tksurfer but I seem to be having difficulties locating the actual defect on the wm volume since I am new to freesurfer.
Cheers, Paula
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Paula, can you send us a snapshot? The inflated surface can have bumps in it, which usually are not a problem. You can also inflate more using the -n switch. From the surf dir:
mris_inflate -n 10 lh.smoothwm lh.inflated
where 10 is the default and you can increase it to get smoother surfaces.
cheers, Bruce
On Wed, 8 Jul 2009 pcraisan@cc.hut.fi wrote:
Hello,
I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried manually removing the bumps one by one by editing the wm volume but it did not have the effect I was hoping for.
Is there an automatic way to smooth the inflated surface? I have tried using mris_smooth but it also messed up my .curv-file in the process.
Best regards, Paula Räisänen
Helsinki University of Technology, Department of Biomedical Engineering and Computational Science
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
pcraisan＠cc.hut.fi -
Pedro Paulo de Magalhães Oliveira Junior