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?
(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
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
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/
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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.
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/
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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
Hi!
You probably mean
mris_expand
which creates a surf inside or outside of white, e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Best, Markus
2014-08-13 20:57 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
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
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
Fantastic - thank you.
Don
Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@gmail.com] Sent: Wednesday, August 13, 2014 3:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] a few short confirmatory questions
Hi!
You probably mean
mris_expand
which creates a surf inside or outside of white, e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Best, Markus
2014-08-13 20:57 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>:
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-mailto:freesurfer- bounces@nmr.mgh.harvard.edumailto:bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, August 13, 2014 2:21 PM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358tel:617-724-2358 Fax: 617-726-7422tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358tel:617-724-2358 Fax: 617-726-7422tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yep, that's it
On 08/13/2014 03:08 PM, Markus Gschwind wrote:
Hi!
You probably mean
mris_expand
which creates a surf inside or outside of white, e.g.
mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border
mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white
Best, Markus
2014-08-13 20:57 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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> [mailto:freesurfer- <mailto:freesurfer-> >> bounces@nmr.mgh.harvard.edu <mailto: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 <mailto: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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto: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 <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
mris_expand
On Aug 13, 2014, at 8:57 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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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