Viewing 5 posts - 1 through 5 (of 5 total)
Viewing 5 posts - 1 through 5 (of 5 total)
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Is there a transformation matrix from patient (e.g., T1 MR) to template that is outputted as part of the normalization procedure? I see matrices outputted for the postopCT to anat_T1 coregistration process.
Thanks for your help,
the deformation into MNI is nonlinear, so a 4×4 matrix would not suffice. There are deformation files in the patient folder with naming schemes depending on which method you used in the normalization step. You can apply the deformation to other nifti files using the Tools menu.
Thanks for your reply Andy. I’ve looked in the patient folder and cannot find these deformation files. I had used ANTs SyN for the patient to template nonlinear coregistration. The matlab files in the patient folder are:
The ea_normmethod_applied file contains only text stating ‘ea_normalize_ants’.
Yes, I’d like to apply the deformation to one of the fiber tracts that I’ve generated and exported as a 3D object using other software. I was able to use SPM to normalize the tract to the MNI/ICBM template and then use add the normalized tract to the 3d scene. However, I’d prefer using the already calculated deformations from lead-DBS.
Thanks for your help.
then the deformation is a .h5 file as created by ANTs. You could simply use this entry from the Tools Menu to warp your fibers into MNI:
Thanks Andy, it worked.
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