Hi Greg,

Have you tried to just apply the bbreg transformation to your tract to double check whether that registration is accurate?

Lilla

On Tue, 10 Jan 2012, Gregory Kirk wrote:

Hi

i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.0 i am thinking the bb register transformation i am using is not the correct one, but it seems the logical choice, but obviously not working good as forceps minor ends up wraped around the brain stem.

here is what i run

mri_vol2vol --targ  /study5/aa-scratch/TEENEMO/freesurfer_subjects/033/mri/norm.mgz --m3z combined_to033_elreg_afteraseg-norm.m3z --noDefM3zPath --fsl /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006//dmri/xfms/diff2anat.bbr.mat --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006/dpath/fminor_PP_avg33_mni_bbr/path.pd.nii.gz --out ./to033path.pd.nii.gz --interp trilin --no-save-reg

thanks

greg

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