Then I am not doing the question propperly, and I obviously did not understand the basis of tksurfer :)
I am going to work in Matlab, and I just wanted to use the output of Freesurfer to help me with my algorithm, so I am not going to use neither tkmedit nor tksurfer. Hence, I do not exactly need to know how to visualize these data correctly in tksurfer :). My needs are in a lower level.
So, the question now is: having a pixel of one of the slices of the original image, how can I know if it is a sulcus, a gyrus or none of those? From what file(s) can I read that information?
Cheers.
Hi Fidel
the surfaces of the same hemi for a given subject area all topologically equivalent and share an index structure. what that means is that the vertex label/annotation can be shown/used on any surface, including the ?h.white and ?h.pial surfaces (which is probably what you want). Or you can look at the aparc+aseg.mgz, which combines the subcortical and cortical labelings into a single volume.
cheers Bruce
On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Thanks mr Fischl, but these surfaces are a deformation of the original brain (According to what I have read in the wiki). My intention is to write an algorithm to do some operations on the original images, using the sulci information from freesurfer. In order to do that, I would need the sulci information IN a segmentation of the brain with the same size as the original. Is there any transformation I can apply to have this information?
Thanks again.
the gyral/sulcal segmentations are generated on the surfaces and viewable in tksurfer. For example:
tksurfer <subject> lh inflated -aparc
will bring up <subject> and show the lh.aparc.annot on top of the inflated surface. You can also load them from the tksurfer interface using file->label->import annotation
cheers Bruce
On Mon, 20 Dec 2010, FIDEL ALFARO ALMAGRO wrote:
Hi,
I am pretty new in freesurfer and I do not know if this question has been answered before (It is difficult to search for 1 basic question), so I will post it anyways:
- Is there any segmentation/labeling in freesurfer that allows the
user to identify all the sulci of an MR image? I have done the recon-all, correctly, but I am not able to see any sulcus using tkmedit with the generated segmentations.
Thanks in advance.
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