Hello there,
We have a subject processed using recon-all that possesses a dimple in the region of the left lateral ventricle. We would like your opinion as to whether or not it requires fixing and how - we are not sure how to go about it (i.e. if it requires a wm.mgz fill how much of it should be filled? It is a tricky subject in that it is quite an asymmetrical brain). This dimple will surely impact upon the mean cortical thickness, a metric which we are interested in using, and therefore we would prefer to fix it if possible.
The dimple is approx at talairach -22.0 -40.5 11.8
I attach some screen shots from tksurfer and tkmedit, although I think it might be best seen from different orientations so let me know if I should upload the subject.
Many thanks,
Rysia
Hi Rysia,
I would look at wm.mgz loaded as auxiliary volume and switch to main volume frequently to see, whether you have anything in wm.mgz, which needs to be fixed. There is a tutorial on fixing wm.mgz on the followning web-page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
I found very useful to go through the recommended workflow as well:
http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction
I hope this helps you a bit.
Best,
Martin
On Wednesday 12 November 2008 13:42:08 Burmicz, Ryzarda wrote:
Hello there,
We have a subject processed using recon-all that possesses a dimple in the region of the left lateral ventricle. We would like your opinion as to whether or not it requires fixing and how - we are not sure how to go about it (i.e. if it requires a wm.mgz fill how much of it should be filled? It is a tricky subject in that it is quite an asymmetrical brain). This dimple will surely impact upon the mean cortical thickness, a metric which we are interested in using, and therefore we would prefer to fix it if possible.
The dimple is approx at talairach -22.0 -40.5 11.8
I attach some screen shots from tksurfer and tkmedit, although I think it might be best seen from different orientations so let me know if I should upload the subject.
Many thanks,
Rysia
it looks okay to me in the slices you sent, but it's hard to tell. Basically you should check the ?h.white surface and see if it follows the true boundary, and if not edit the wm.mgz to add/delete voxels
cheers, Bruce
p.s. if you are still not sure, tar and gzip the subject and drop it on our site
On Wed, 12 Nov 2008, Burmicz, Ryzarda wrote:
Hello there,
We have a subject processed using recon-all that possesses a dimple in the region of the left lateral ventricle. We would like your opinion as to whether or not it requires fixing and how - we are not sure how to go about it (i.e. if it requires a wm.mgz fill how much of it should be filled? It is a tricky subject in that it is quite an asymmetrical brain). This dimple will surely impact upon the mean cortical thickness, a metric which we are interested in using, and therefore we would prefer to fix it if possible.
The dimple is approx at talairach -22.0 -40.5 11.8
I attach some screen shots from tksurfer and tkmedit, although I think it might be best seen from different orientations so let me know if I should upload the subject.
Many thanks,
Rysia
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Burmicz, Ryzarda -
Martin Kavec