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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@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 <gr...@nmr.mgh.harvard.edu<mailto: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> >> [mailto:freesurfer-<mailto:freesurfer-> >> boun...@nmr.mgh.harvard.edu<mailto: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<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 >> gr...@nmr.mgh.harvard.edu<mailto:gr...@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 gr...@nmr.mgh.harvard.edu<mailto:gr...@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
