Dear Doug I think my problem may caused by that extracted ROI have different coordination to original T1 image, although they match well in freeview. For example, one voxel is [148,144,131] in extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how to extract a ROI having same coordinate with T1?
Regards Cong
From: Douglas Greve greve@nmr.mgh.harvard.edu
no idea. you'll proably have to contact the MRIcro group
On 5/16/17 8:28 AM, Cong wrote:
Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: / mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii/ I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and it looks well. However, when I overlaid l_thal.nii to control001.nii in Windows MRIcro, it comes a Warning: this NIFTI image includes an rotation transformation. When I open these two files same time, the left thalamus mismatch obviously to original T1 image. I attached an image to show my problem. I try to register this ROI volume to diffusion B0 image, and the registered left thalamus appears in the same wrong position as shown in attached image. Could someone tell me what?s wrong and how to solve it.
Regards Cong
try this https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 5/16/17 12:34 PM, Cong wrote:
Dear Doug I think my problem may caused by that extracted ROI have different coordination to original T1 image, although they match well in freeview. For example, one voxel is [148,144,131] in extracted left thalamus but [71,130,89] in original T1.nii and T1.mgz. So how to extract a ROI having same coordinate with T1?
Regards Cong
From: Douglas Greve greve@nmr.mgh.harvard.edu
no idea. you'll proably have to contact the MRIcro group
On 5/16/17 8:28 AM, Cong wrote:
Dear FSers I extracted left thalamus as ROI volume from aseg.mgz by this command: / mri_binarize --i control001/mri/aseg.mgz --match 10 --o control001/roi/l_thal.nii/ I overlaid l_thal.nii to control001.nii in MRIcro software in a Macbook and it looks well. However, when I overlaid l_thal.nii to control001.nii in Windows MRIcro, it comes a Warning: this NIFTI image includes an rotation transformation. When I open these two files same time, the left thalamus mismatch obviously to original T1 image. I attached an image to show my problem. I try to register this ROI volume to diffusion B0 image, and the registered left thalamus appears in the same wrong position as shown in attached image. Could someone tell me what?s wrong and how to solve it.
Regards Cong
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Cong -
Douglas Greve