I'm registering a subject to cvs_avg35_inMNI152 using mri_cvs_register. My command is:
mri_cvs_register --mov patient --template cvs_avg35_inMNI152 --m3d --nocleanup --openmp 8 --keepelreg --hemi lh Then I'm using applymorph to apply the resulting warp (combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d) to a set of voxel coordinates from the patient's orig volume. applyMorph --template cvs_avg35_inMNI152/mri/brain.mgz --transform combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d point_list vox_points_in_orig.txt warp_vox_points.txt linear and if I save those coordinates output in warp_vox_points.txt in a nifti volume with the same affine and header as final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz, I see that the points are way posterior to the warped brain. Has anyone else had this issue with applymorph? and do you happen to know what the cause might be? Thanks for your help and let me know if I can give more details. (fyi I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 on a linux server with Ubuntu 12.04.4) -zack
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