Dear FreeSurfer team
I am correcting some structural MRI scans after the automated surface-based
analysis and the automated segmentation.
I would like to know if you have any information about how often the Voxel Edit
is used and if it makes sense to correct the subcortical segmentation. I have
And in your second set of images, you probably need to edit the wm.mgz.
I suspect that there is a topology problem that is messing up the wm.orig
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorder
Hi Jon
usually this happens because the wm in the wm.mgz doesn't extend out far
enough. Is that the case here? If not, you can also try direct
repositioning in freeview under tools->reposition surface.
cheers
Bruce
p.s. we also have some newer tools that I've been working on that can use a
I'm wondering about how to best approach two similar problems with pial
surfaces. In one case I'd like to extend it and in the other I'd like to
reduce it (for lack of a better term)
These first two images are from a brain in which I'd like to extend the
surface.
http://i.imgur.com/ziDQd.png
http:
Hi Julia,
Are you editing on a Mac?
-Louis
On Thu, 22 Mar 2012, Richter, Julia wrote:
> Hi freesurfer experts,
>
> I am trying to correct the pial surfaces of my data. I was able to remove
> voxels with the right button of my mouse, but unfortunately, it didn't work
> out to add voxels. Can som
Hi Julia
it's really hard to tell from just this image. If the problem is the
skull strip removing voxels you can use the "clone" tool to paint them
back in from another volume like the T1.mgz. Are you sure it's not dura or
pial vessels? Where in the brain do you mean?
cheers
Bruce
On Thu, 22
Hi freesurfer experts,
I am trying to correct the pial surfaces of my data. I was able to remove
voxels with the right button of my mouse, but unfortunately, it didn't work out
to add voxels. Can somebody please help me with that? Do I need a middle button
on the mouse for it?
Attached you may
better to do it from inside recon-all so as to get it's bookkeeping. Run
with -finalsurfs
doug
Brian T. Quinn wrote:
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a ne
hi Lars-
perhaps you need to delete more voxels. make sure you're editting the
brain volume, and you can just run make_final_surfaces if you only
want to regenerate a new pial surface (takes [a lot] less time).
thanks,
brian
On Mon, 12 Sep 2005, Lars Tjelta Westlye wrote:
Dear all,
I am t
Dear all,
I am trying to edit the pial surface by editing/deleting voxels in the
brain volume within the pial surface ('labeled' as a part of cortex), but
clearly are parts of dura when manually inspected. When I rerun the last
automatic procedures (fix, make_final, morph), and check the pial surf
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