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
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>
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:
2009/8/18 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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
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>>>
>
> 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>>>>
>
>
> 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
> ------------------------------------------------------------------------
>
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>
> -- 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>>
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> <mailto:greve@nmr.mgh.harvard.edu
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>
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>
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>
>
>
>
> --
> 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:
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>
>
>
--
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
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