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 <gr...@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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > >> boun...@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 > >> gr...@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 > gr...@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 >
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