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
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:
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>
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, zcoordinates. (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. Thatis to
say, the cortical thickness should superimposed on atemplate
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.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto: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 withthe many
voxels containing A group > B group > C group and Agroup < B
group < C group, Freesurfer can’t do that. So, we wantto get
this map by myself and use Matlab or other tool to obtain that. And, now I want to obtain a file that containingthe Tal
coordinate and the thickness value of this coordinatefor all
subjects. Would you tell me how to get the file that containingthe 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 --trgsubjectnoise0.5_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 changelh.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 coordinateof 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.edumailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edumailto: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/BugReportinghttp://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/BugReportinghttp://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 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
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
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:
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>
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, zcoordinates. (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. Thatis to
say, the cortical thickness should superimposed on atemplate
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.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto: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 withthe many
voxels containing A group > B group > C group and Agroup < B
group < C group, Freesurfer can?t do that. So, we wantto get
this map by myself and use Matlab or other tool to obtain that. And, now I want to obtain a file that containingthe Tal
coordinate and the thickness value of this coordinatefor all
subjects. Would you tell me how to get the file that containingthe 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 --trgsubjectnoise0.5_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 changelh.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 coordinateof 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.edumailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edumailto: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/BugReportinghttp://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/BugReportinghttp://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 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
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
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
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:
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>
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, zcoordinates. (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. Thatis to
say, the cortical thickness should superimposed on atemplate
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.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edumailto: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 withthe many
voxels containing A group > B group > C group and Agroup < B
group < C group, Freesurfer can?t do that. So, we wantto get
this map by myself and use Matlab or other tool to obtain that. And, now I want to obtain a file that containingthe Tal
coordinate and the thickness value of this coordinatefor all
subjects. Would you tell me how to get the file that containingthe 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 --trgsubjectnoise0.5_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 changelh.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 coordinateof 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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<mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu>
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<mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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/BugReportinghttp://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/BugReportinghttp://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 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 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
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
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
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:
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>
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 >
> > _______________________________________________ > 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 > 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 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 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Feng-Xian Yan