Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ?
I am looking forward to your reply. Thank you very much !
Best Wishes, Zhiqiang Sha
Hi Zhiqiang
(1) No, the manual parcellations were done in individual subject space, then compiled into an atlas in fsaverage/spherical warp coords.
(2) We inflate the white surface, but I don't think inflating the pial would be much different. YOu can do it yourself if you want with mris_inflate
(3) No, this converts it to individual subject space. You could transform it to MNI with mri_vol2vol using the talairach.xfm that is in the subjects mri/transforms dir.
cheers Bruce
On Sun, 15 Oct 2017, Zhiqiang Sha wrote:
Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ?
I am looking forward to your reply. Thank you very much !
Best Wishes, Zhiqiang Sha
【网易自营】好吃到爆！鲜香弹滑加热即食，经典13香/麻辣小龙虾仅75元3斤>>
Thanks for your quick reply. For the third question, if I use talairach.xfm to transform the atlas in volume, it will go to the MNI305 space. However, how to transform the atlas from the Talariach to MNI152 space? And I will the atlas in volume format in other software related to the functional MRI. Thank you for the great help ! At 2017-10-15 23:35:58, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Zhiqiang
(1) No, the manual parcellations were done in individual subject space, then compiled into an atlas in fsaverage/spherical warp coords.
(2) We inflate the white surface, but I don't think inflating the pial would be much different. YOu can do it yourself if you want with mris_inflate
(3) No, this converts it to individual subject space. You could transform it to MNI with mri_vol2vol using the talairach.xfm that is in the subjects mri/transforms dir.
cheers Bruce
On Sun, 15 Oct 2017, Zhiqiang Sha wrote:
Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ?
I am looking forward to your reply. Thank you very much !
Best Wishes, Zhiqiang Sha
【网易自营】好吃到爆！鲜香弹滑加热即食，经典13香/麻辣小龙虾仅75元3斤>>
do you really want the atlas in MNI space or do you want an individual subject parcellation mapped to MNI? If the atlas, I think it already is, or at least it lives on the fsaverage surface which has associated MNI coords. Doug can confirm.
cheers Bruce
On Mon, 16 Oct 2017, cain wrote:
Thanks for your quick reply. For the third question, if I use talairach.xfm to transform the atlas in volume, it will go to the MNI305 space. However, how to transform the atlas from the Talariach to MNI152 space? And I will the atlas in volume format in other software related to the functional MRI. Thank you for the great help ! At 2017-10-15 23:35:58, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Zhiqiang
(1) No, the manual parcellations were done in individual subject space, then compiled into an atlas in fsaverage/spherical warp coords.
(2) We inflate the white surface, but I don't think inflating the pial would be much different. YOu can do it yourself if you want with mris_inflate
(3) No, this converts it to individual subject space. You could transform it to MNI with mri_vol2vol using the talairach.xfm that is in the subjects mri/transforms dir.
cheers Bruce
On Sun, 15 Oct 2017, Zhiqiang Sha wrote:
Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ?
I am looking forward to your reply. Thank you very much !
Best Wishes, Zhiqiang Sha
【网易自营】好吃到爆！鲜香弹滑加热即食，经典13香/麻辣小龙虾仅75元3斤>>
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