25 Aug
2009
25 Aug
'09
11:26 a.m.
you have to map the subject/surf/lh.thickness to fsaverage space as well (again with mri_surf2surf).
doug
Feng-Xian Yan wrote:
2009/8/25 Feng-Xian Yan <mimigirln@gmail.com mailto:mimigirln@gmail.com>
Hi, First, I use mri_surf2surf (as follows) to map our subjects to fsaverage. mri_surf2surf –srcsubject subject --sval-tal-xyz white --hemi lh --trgsubject fsaverage --tval-xyz --tval lh.subject.tal Next step, I use mris_convert to show the cortical thickness value of this subject on this MNI coordinates. But, this has an error as follows. mris_convert -c subject/surf/lh.thickness fsaverage /surf/lh.white lh.subject.thickness.asc ERROR: number of vertices in subject/surf/lh.thickness does not match surface (154962,163842) I know what’s happen, but I don’t know how to solve. I want to obtain the asc file containing the same vertices as fsaverage and with the cortical thickness value and their coordinates in the file. Could you teach me how to obtain the match fsaverage surface file? Thank you in advance! Feng-Xian 2009/8/20 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> 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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <mimigirln@gmail.com <mailto:mimigirln@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>>> > <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 <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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