Dear Bruce, Now I can get thickness values, vertex locations and the faces. But it seems every subject has a different number of vertices. In my case Subject1 has 107107 vertices, whereas Subject2 has 133093. Is it possible to normalized the subjects into same space?
Thanks for the all help. sincerely yours, Onur ________________________________ Gönderen: Onur Uğurlu <t_mac_o...@hotmail.com> adına freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> Gönderildi: 25 Aralık 2016 Pazar 23:56 Kime: Freesurfer support list Konu: [Freesurfer] Ynt: Ynt: Ynt: Ynt: Neighborhood of a vertex Hi Bruce; It works! I didn't know that it's a scalar. Thanks for the help. sincerely yours, Onur ________________________________ Gönderen: Bruce Fischl <fis...@nmr.mgh.harvard.edu> adına freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> Gönderildi: 23 Aralık 2016 Cuma 22:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Ynt: Neighborhood of a vertex Thickness isn't a surface, it's a scalar field. Use read_curv for it On Dec 23, 2016, at 11:09 AM, Onur Uğurlu <t_mac_o...@hotmail.com<mailto:t_mac_o...@hotmail.com>> wrote: Hi Bruce; Unfortunately still we have the same problem. I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52 I also executed "recon-all -make all" script as you suggested but nothing changed. When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double Any ideas? ________________________________ Gönderen: Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> adına freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed On Tue, 20 Dec 2016, Onur Uğurlu wrote: > > Hi Bruce, > > > I am using lh.orig file located in "surf" directory after running recon-all > script with -qcache option, and trying to match this data with lh.thickness > file again in the same directory. Am I using a wrong combination ? > > > sincerely yours, > > Onur > > > ____________________________________________________________________________ > Gönderen: Bruce Fischl > <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> adına > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > Gönderildi: 19 Aralık 2016 Pazartesi 19:48 > Kime: Freesurfer support list > Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex > that shouldn't be the case. Run mris_info or mris_euler_number on your > input surface. Can you load the thickness as a surface overlay? It may be > that you regenerated surface and not the htickness, or visa-versa. Which > surface are you using? > > On Mon, 19 Dec 2016, Onur Uğurlu wrote: > > > > > Hi Bruce, > > > > > > Thank you so much for the answer. > > > > > > I have used "read_surf.m" function and got the list of vertex locations > and > > a list of faces. However, the list contains 107106 vertices whereas the > > lh.thickness.asc file contains 118603 vertices. How can I match the > > thickness values which are inlh.thickness.asc file with the vertices which > > were obtained from "read_surf.m" function? > > > > > > Sincerely yours, > > > > Onur > > > > > >___________________________________________________________________________ > _ > > Gönderen: Bruce Fischl > > <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> adına > > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > > Gönderildi: 18 Aralık 2016 Pazar 17:54 > > Kime: Freesurfer support list > > Konu: Re: [Freesurfer] Neighborhood of a vertex > > Hi Onur > > > > for that you need a surface file. If you are using matlab you can load a > > surface file in with read_surf.m. The <vertex index> will then be an index > > into the surface (although note that you will need to add 1 to it since > > matlab is 1-based when you index into the vertex list). It will return a > > list of vertex locations and also a list of faces. The faces contain the > > (0-based) indices of the vertices in each triangle, which can be used to > > compile a list of neighbors. > > > > cheers > > Bruce > > > > > > > > On Sun, 18 Dec 2016, Onur Uğurlu wrote: > > > > > > > > Hi all, > > > > > > > > > I have a 'lh.thickness.asc' file which contains thickness values of each > > > vertex. > > > > > > The format of the file is following; > > > > > > <vertex index> <x> <y> <z> <thickness> > > > > > > However, x,y,z are not integer. What is the unit of the x,y,z values in > > the > > > file? I am trying to find all the neighborhood of any given vertex as > > x,y,z > > > -> x+1,y,z etc, can you suggest a method for this problem. > > > > > > > > > Sincerely yours, > > > > > > Onur > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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