Try these commands: mri_surf2surf --s subject --hemi lh --sval-tal-xyz white --tval-xyz --tval lh.white.tal mris_convert lh.white.tal lh.white.tal.asc
doug Feng-Xian Yan wrote: > > Hi, > > I have some problems want to understand. > > > > (1) I want to analysis the cortical thickness difference of three > groups. But, three groups (one factor/three levels) of Freesurfer is > not satisfied with our demand. Because we want to get a thickness > difference map that satisfied with the many voxels containing A group > > B group > C group and A group < B group < C group, Freesurfer can’t > do that. So, we want to get this map by myself and use Matlab or other > tool to obtain that. And, now I want to obtain a file that containing > the Tal coordinate and the thickness value of this coordinate for all > subjects. > > Would you tell me how to get the file that containing the Tal > coordinate and the thickness value of this coordinate? > > > > (2) Before, I want to use the following command to get the thickness > value. > > The command line is "mri_surf2surf --srcsubject noise0.5_0 > --srcsurfval thickness --sfmt surface --trgsubject noise0.5_0 > --trgsurfval noise0.5_0_tal.xfm --tfmt surface --hemi lh > --sval-tal-xyz orig --tval-xyz", and then i type “mris_convert > lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. > > But, the result file(lh.thickness.asc) does not contain the thickness > value of this coordinate. > > So, I think these commands have some error. > > > > (3) Use the command “mris_convert –c lh.thickness lh.white > lh.thickness.asc” to obtain the thickness value of the RAS > coordinates. But, I’m confused about that if I change lh.white to > lh.pail or lh.inflated. > What’s difference for the three? > > > > (4) And, I ask some problem before. > > Everyone said the result file(lh.thickness.asc) is using RAS > coordinates through “mris_convert –c lh.thickness lh.white > lh.thickness.asc”. But, I have confused about this. When I open this > subject by tksurfer, I look at the coordinate of the vertex RAS in the > tksurfer tool box, and the coordinate is difference from the > coordinates that obtain from the command “mris_convert –c lh.thickness > lh.white lh.thickness.asc”. > So, which one is right? > > > > Thank you in advance! > > > > Feng-Xian > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
