Re: [Freesurfer] Ascii file of thickness overlay with vertex index and coordinates

Hi Mike you can convert the surfaces to ascii also, but I don't think we have a single format that is what you describe (since the thickness itself is not a property of any single surface). Easy enough to do in matlab though if you read in whatever surface and thickness file you want. cheers

[Freesurfer] Ascii file of thickness overlay with vertex index and coordinates

Hi, I was wondering how I would go about getting the vertex index and coordinates in one ascii file for a thickness overlay file. With mri_convert using the --asci+crsf option it outputs the vertex index only. Now I want to get the coordinates of each index...Is this possible? I may be misunderst

Re: [Freesurfer] ascii file

what is your new command line? Feng-Xian Yan wrote: > Hi, >I change the input and output from curv to surface, but the error > is the same. > So, how do I do to resolve it? > > Thank you in advance! > > Feng-Xian > > > > > 2009/8/5 Douglas N Greve >

Re: [Freesurfer] ascii file

Hi, I change the input and output from curv to surface, but the error is the same. So, how do I do to resolve it? Thank you in advance! Feng-Xian 2009/8/5 Douglas N Greve > The output is not a curvature file, it is a surface. > > doug > > Feng-Xian Yan wrote: > > > > Hi, > > > > I try ag

Re: [Freesurfer] ascii file

The output is not a curvature file, it is a surface. doug Feng-Xian Yan wrote: > > Hi, > > I try again with you said. First, I type this command“mri_surf2surf > --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv > --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv > --hem

Re: [Freesurfer] ascii file

Hi, I try again with you said. First, I type this command“mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert -c lh.noise0.5_0_tal.xfm lh

Re: [Freesurfer] ascii file

you need to tell it what format to write the output in. Try using - --tfmt curv I would have thought you needed --sfmt curv also. I'm just guessing though. Doug is the expert on this. cheers, Bruce On Tue, 4 Aug 2009, Feng-Xian Yan wrote: > Hi, > > I had asked two problems before; one is wh

[Freesurfer] ascii file

Hi, I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with

Re: [Freesurfer] ascii file

Hi Feng-Xian, the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm. cheers, Bruce On Mon, 20 Jul 2009, Feng-Xian wrote: > > Hi, > I have two problems want to solve. > First, I want to know what coordinates it is, when I type t

[Freesurfer] ascii file

Hi, I have two problems want to solve. First, I want to know what coordinates it is, when I type the following command. mris_convert -c lh.thickness lh.white lh.thickness.asc Is it Tal coordinate?? Second, if the asc file doesn't use Tal coordinate, what commands do I type to obtain