Paul,
Thanks for your response.
For the convertwarp usage with premat and postmat (convertwarp --ref=refvol --premat=mat1 --warp1=vol1 --warp2=vol2 --postmat=mat2 --out=output_warp) I'm not sure which files to pass as arguments. From the non-linear MNI->T1 transformation, I have the affine transformation matrix (affine.mat), the non-linear transformation image file (MNI152_FNIRTed.nii.gz) and the MNI image to which the transformation has been applied using applywarp (MNI_in_T1.nii.gz). From the linear T1->DWI, I have the transformation matrix (T1_in_DWI.mat) and the transformed T1 image (T1_in_DWI.nii.gz). Any pointers are much appreciated. As a reminder, the end goal is a transformation from MNI to subject DWI space.
Thanks,
Suraj
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