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
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent
>> to you in error but does not contain patient information, please contact the
>> sender and properly dispose of the e-mail.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer