Hi all, I have fMRI data in individual space, converted to individual surface using vol2surf and to fsaverage surface using surf2surf (commands [1] and [2] below). With Matlab, I obtain the vertex with the maximum value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152 coordinate of this vertex (for comparison with the literature), I think I have two options:
1.- Work in the individual space: >> max_SurfaceRAS = lhwhite(max_Vtx, :); >> max_RAS = T1.vox2ras*inv(T1.tkrvox2ras)*[max_SurfaceRAS';1]; I can check in freeview that the result is correct. >> max_RAS305 = TalXFM * max_RAS; I can check in tkmedit that this is right too. At last, using the MNI305to152 matrix provided by Doug in the wiki: >> max_RAS152 = MNI305to152 * max_RAS305;
2.- Work in the fsaverage (305) space >> max_SurfaceRAS305 = lhwhite305(max_Vtx305, :); as Surface RAS is the same as RAS, we only have to convert it to 152 >> max_RAS152_305 = MNI305to152 * max_SurfaceRAS305 ;
The results are: For 1: [-15.57, -93.62, -2.84] For 2: [-23.06, -97.06, 1.35]
Is this method ok? is this the way it should work? As the results are not the same, is one of the methods inherently better than the other? Many thanks! Gari
[1] mri_vol2surf --srcsubject S001 --projfrac 0.5 --interp trilinear --hemi lh --regheader S001 --mov fMRI.img --o fMRI.mgh
[2] mri_surf2surf --srcsubject S001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval fMRI.mgh --tval fMRI305.mgh --sfmt curv --noreshape --no-cortex
Hi Gari, those look correct (make sure that your indices are not off by 1 (ie, FS uses 0-based indexing, and matlab uses 1-based). I would not expect them to be the same since #1 includes a non-linear transform, and they are only off by about 1.5cm (not bad by affine standards). Not sure that one is better than the other, but #2 is probably more like what is in the liturature.
On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote:
Hi all, I have fMRI data in individual space, converted to individual surface using vol2surf and to fsaverage surface using surf2surf (commands [1] and [2] below). With Matlab, I obtain the vertex with the maximum value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152 coordinate of this vertex (for comparison with the literature), I think I have two options:
1.- Work in the individual space: >> max_SurfaceRAS = lhwhite(max_Vtx, :); >> max_RAS = T1.vox2ras*inv(T1.tkrvox2ras)*[max_SurfaceRAS';1]; I can check in freeview that the result is correct. >> max_RAS305 = TalXFM * max_RAS; I can check in tkmedit that this is right too. At last, using the MNI305to152 matrix provided by Doug in the wiki: >> max_RAS152 = MNI305to152 * max_RAS305;
2.- Work in the fsaverage (305) space >> max_SurfaceRAS305 = lhwhite305(max_Vtx305, :); as Surface RAS is the same as RAS, we only have to convert it to 152 >> max_RAS152_305 = MNI305to152 * max_SurfaceRAS305 ;
The results are: For 1: [-15.57, -93.62, -2.84] For 2: [-23.06, -97.06, 1.35]
Is this method ok? is this the way it should work? As the results are not the same, is one of the methods inherently better than the other? Many thanks! Gari
[1] mri_vol2surf --srcsubject S001 --projfrac 0.5 --interp trilinear --hemi lh --regheader S001 --mov fMRI.img --o fMRI.mgh
[2] mri_surf2surf --srcsubject S001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval fMRI.mgh --tval fMRI305.mgh --sfmt curv --noreshape --no-cortex
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Thanks Doug, this answers the question. I will use the fsaverage data for between subject comparison and literature comparison then. Thanks! Gari PS: yes, the +1 and the xy flipping thing are a real pita :)
On Fri, Nov 18, 2016 at 5:54 PM Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Gari, those look correct (make sure that your indices are not off by 1 (ie, FS uses 0-based indexing, and matlab uses 1-based). I would not expect them to be the same since #1 includes a non-linear transform, and they are only off by about 1.5cm (not bad by affine standards). Not sure that one is better than the other, but #2 is probably more like what is in the liturature.
On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote:
Hi all, I have fMRI data in individual space, converted to individual surface using vol2surf and to fsaverage surface using surf2surf (commands [1] and [2] below). With Matlab, I obtain the vertex with the maximum value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152 coordinate of this vertex (for comparison with the literature), I think I have two options:
1.- Work in the individual space: >> max_SurfaceRAS = lhwhite(max_Vtx, :); >> max_RAS = T1.vox2ras*inv(T1.tkrvox2ras)*[max_SurfaceRAS';1]; I can check in freeview that the result is correct. >> max_RAS305 = TalXFM * max_RAS; I can check in tkmedit that this is right too. At last, using the MNI305to152 matrix provided by Doug in the wiki: >> max_RAS152 = MNI305to152 * max_RAS305;
2.- Work in the fsaverage (305) space >> max_SurfaceRAS305 = lhwhite305(max_Vtx305, :); as Surface RAS is the same as RAS, we only have to convert it to
152
>> max_RAS152_305 = MNI305to152 * max_SurfaceRAS305 ;The results are: For 1: [-15.57, -93.62, -2.84] For 2: [-23.06, -97.06, 1.35]
Is this method ok? is this the way it should work? As the results are not the same, is one of the methods inherently better than the other? Many thanks! Gari
[1] mri_vol2surf --srcsubject S001 --projfrac 0.5 --interp trilinear --hemi lh --regheader S001 --mov fMRI.img --o fMRI.mgh
[2] mri_surf2surf --srcsubject S001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --sval fMRI.mgh --tval fMRI305.mgh --sfmt curv --noreshape --no-cortex
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