you can use mri_surf2surf to map them all the fsaverage, then mris_convert to convert each one to asciii.
cheers Bruce On Thu, 20 Aug 2009, Feng-Xian Yan wrote: > Hi, > > But I want to obtain the asc file or other files containing the same > vertices and with the cortical thickness value and their coordinates in the > file. > > Could some ways to obtain? > > > > Thank you in advance! > > > > Feng-Xian > > > > > 2009/8/20 Doug Greve <gr...@nmr.mgh.harvard.edu> > >> >> 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
