That command is right but add --fstarg or --targ $SUBJECTS_DIR/subject/mri/orig.mgz (they will do the same thing, one is just easier but more obscure than the other)

doug

On 04/23/2014 04:22 PM, Emad Ahmadi wrote:

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 mailto:emad@nmr.mgh.harvard.edu

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