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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Feng-Xian Yan