Hello,
I’m having a volume (e.g. dtifit_FA.nii.gz) and a transform matrix (e.g. diff2anatorig.bbr.mat), and I want to apply the transform matrix to the image and generate a transformed image. This is a general question I’m having, but in this particular case, I want to apply the transform matrix (from diffusion space to the anatomical space generated by TRACULA) to the FA map to generate a transformed FA map that can be overlaid on the anatomical images.
I wonder if I have to use mri_vol2vol command for doing this, and I don’t know how to provide it with appropriate flags. I’m already having the transform matrix generated by TRACULA (and I don’t want to change it; I just want to apply it to the image!). My crude guess would be something like this:
mri_vol2vol --mov <address of dtifit_FA.nii.gz> --o <address of transformed_dtifit_FA.nii.gz> --reg diff2anatorig.bbr.mat
Please let me know how I should run this command.
Thank you very much, Emad
P.S. I know that for this particular example, I can use the anatomical images in dlabel/diff, but the point for me is to learn how to apply a transform matrix to an image and generate a transformed image in freesurfer
Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu