You need a program whose name I can't remember. Bruce, what is the name of the program to create a surface midway between white and pial?
Don, you can use this to create the mid surface (or project it to any depth) and to create a surface that is just inside the WM (use a negative projection distance). Then when you run mri_annotation2label specify each of these surfaces with --surf (you'll have to run it twice to get labels for each surface)
On 08/13/2014 02:31 PM, Krieger, Donald N. wrote:
Thanks for posting back so quickly and for the clarifications. What I am looking for is a list of vectors which are in the gray matter and a 2nd list that are inside the nearby white matter.
It sounds like the "white" are inside the white matter but near the boundary with the gray. Is it reasonable to rely on each of these to be inside the white matter for at least say 1/2 mm in all directions from its xyz coordinate?
You mention lists of nearest neighbors ... where may these be found as I definitely would like to use them or else likely must generate my own. In order to get the coordinates of a vector within the nearby gray matter, I was thinking to use a neighbor, perhaps not nearest but certainly close, in the direction of the nearest "pial" vector. What do you think?
An alternative is to use a nearby vector from the list in "ribbon" for the gray matter.
Regards,
Don
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, August 13, 2014 2:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] a few short confirmatory questions
On 08/13/2014 02:11 PM, Krieger, Donald N. wrote:
mri_annotation2label enables extraction of vectors from .annot files to .label files, one file per label.
One may choose orig, white, or pial vectors.
(1)orig vectors are on the cortical surface. The gray scale value for each of these is that of gray matter, correct? And these are inside the pia and outside "white," correct?
orig is the first surface created by tessellating the white matter. It is a coarse, jagged surface on the voxel boundary. The white is the orig refined to follow the GM/WM boundary better. The orig is definitely inside the pia, but one cannot make a statement about its position relative to the white. I don't know what you mean by the gray scale value. The surface just has xyz values and lists of nearest neighbors.
(2)white vectors are at the surface of the white matter just below the "orig" layer, correct? Their gray scale value is that of white matter, correct?
Thanks,
Don
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