Yes, this is what our group analysis tools do. You can find tutorials on the wiki. You'll probably start with mris_preproc.
doug On Thu, 20 Aug 2009, Feng-Xian Yan wrote: > Hi, > > Thank you for your responses before. > > > > I have another problem want to solve. I check the number of vertex for all > subjects, but I found that the number of vertex for each subjects and each > hemispheres is different. Because I want to compare cortical thickness using > vertex-by-vertex, I would to obtain the same vertex number. > > Therefore, have something to do to obtain the same vertex number, i.e. > template the cortical thickness at each vertex for each subject on the > fsaverage surface, or other methods? > > > > How can I do? Would you get me a hand? > > > > Thank you in advance! > > > > Feng-Xian > > > > > 2009/8/18 Feng-Xian Yan <mimigi...@gmail.com> > >> >> Thank s for your response. >> >> So, the coordinates are MNI coordinates, not Talairach coordinates. >> >> >> >> Thank you in advance. >> >> >> >> Feng-Xian >> >> >> >> 2009/8/18 Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> >>> The values in the asc file are in MNI305 space. You can see this in >>> tksurfer with View->Configure->Information and select the mni305 button. >>> >>> Feng-Xian Yan wrote: >>> >>>> >>>> Thank you for your response. >>>> >>>> So, you mean that I have to do "mris_convert" two times. One for >>>> lh.white.tal.asc, another for lh.thickness.asc. And the Tal coordinates in >>>> lh.white.tal.asc file corresponds to the cortical thickness value in >>>> lh.thickness.asc file. >>>> >>>> >>>> But, the Tal coordinates in lh.white.tal.asc is difference from the >>>> result in the tksurfer tool box. That is to say, when I open this subject >>>> by >>>> tksurfer, I look at the coordinate of the vertex Tal 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?. >>>> >>>> >>>> What do have some problems? >>>> >>>> >>>> Thank you in advance! >>>> >>>> >>>> Feng-Xian >>>> >>>> >>>> 2009/8/18 Douglas N Greve <gr...@nmr.mgh.harvard.edu <mailto: >>>> gr...@nmr.mgh.harvard.edu>> >>>> >>>> You have convert the thickness file (lh.thickness) to ascii like >>>> you did >>>> with the surface (with mris_convert). You will then have two >>>> files, and >>>> the second file will have the thickness values. >>>> >>>> doug >>>> >>>> Feng-Xian Yan wrote: >>>> > >>>> > Hi, >>>> > >>>> > Sorry, I don't know what you mean. I know each lines is a vertex and >>>> > represent a Tal coordinate, but each lines only contain xyz, but not >>>> > contain cortical thickness value of these coordinates. That is >>>> to say, >>>> > the following is >>>> > >>>> > Tal x Tal y Tal z >>>> > >>>> > -13.424789 -125.068245 12.671550 0 >>>> > >>>> > What?s wrong do I think? >>>> > >>>> > Thank you in advance. >>>> > >>>> > Feng-Xian >>>> > >>>> > 2009/8/18 Douglas N Greve <gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>>> >>>> > >>>> > Just convert the lh.thickness to ascii as well. Each line of the >>>> > xyz coords corresponds to a line in the thickness ascii >>>> (each line >>>> > is a vertex). >>>> > >>>> > >>>> > doug >>>> > >>>> > Feng-Xian Yan wrote: >>>> > >>>> > >>>> > Hi, >>>> > >>>> > I try it again with you recommend me, but the produced asc >>>> > file (lh.white.tal.asc) only contain x, y, z >>>> coordinates. (The >>>> > following shows that.) >>>> > >>>> > >>>> > #!ascii version of lh.white.tal >>>> > >>>> > 155006 310008 >>>> > >>>> > -13.424789 -125.068245 12.671550 0 >>>> > >>>> > -13.939213 -125.063232 12.714314 0 >>>> > >>>> > -14.861158 -125.268639 12.404987 0 >>>> > >>>> > >>>> > >>>> > But, I want to have cortical thickness value with Tal >>>> > coordinates. This file doesn?t satisfy our demand. >>>> > >>>> > >>>> > Our demand should contain two points. >>>> > >>>> > 1) Each vertex across the mantle was represented with an >>>> > estimated value of cortical thickness and these estimated >>>> > values of cortical thickness should have their coordinates. >>>> > >>>> > 2) We want to analysis the cortical thickness difference of >>>> > three groups, so we want to the cortical thickness value of >>>> > each vertex across each subjects should be matched. That >>>> is to >>>> > say, the cortical thickness should superimposed on a >>>> template >>>> > surface like fsaverage. >>>> > >>>> > Therefore, how do we do to obtain the asc file matching our >>>> > demands? >>>> > >>>> > >>>> > Thank you in advance. >>>> > >>>> > >>>> > Feng-Xian >>>> > >>>> > >>>> > >>>> > >>>> > 2009/8/14 Douglas N Greve <gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu>>>> >>>> > >>>> > >>>> > 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 >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >>>> > <mailto:Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> > <mailto: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> >>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.edu> >>>> > <mailto:gr...@nmr.mgh.harvard.edu >>>> <mailto: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 >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> > >>>> > >>>> > >>>> > -- >>>> > Douglas N. Greve, Ph.D. >>>> > MGH-NMR Center >>>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>> <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> > >>>> > >>>> > >>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> gr...@nmr.mgh.harvard.edu <mailto: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 >>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>>> >>>> >>>> >>>> >>> -- >>> 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 >>> >>> >>> >> > -- 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
