I’m looking for some guidance in performing tckgen with an anatomical mask as the seed image. I’m having trouble moving my mask into the native diffusion space before running tckgen. My mask is a grey matter, binary and is in MNI space.
I attempted to move my masks into native space of the DWI by executing the following:
flirt -in Preprocessed_DWI.nii.gz -ref MNI_152_Template.nii.gz -dof 6 -omat move.mat
transformconvert move.mat Preprocessed_DWI.nii.gz MNI_152_Template.nii.gz flirt_import move.txt
mrtransform mask_MNI.nii.gz -linear move.txt mask_Native.nii.gz -inverse
My thought was that I would move the DWI into MNI space and apply the inverse of that rigid transform to the mask, but its location appears to be way off.
Any guidance or advice would be greatly appreciated.