Dear List,
Pre-aligning images to the MNI template prior to segmentation for volumetry has been discussed on the list before and can improve segmentation depending on the particulars of the data set. I tried this with a rigid body + linear scaling transform, using 'Check Reg' and 'Reorient'. After applying the transform/reorientation to the image the transform is saved in the nifti sform fields as expected.
I didn't expect the voxel size in the header to also change - is this correct?
For example, applying a scaling of 0.9 to a template image changes the voxel size, sform and qform as follows:
nifti_tool -diff_hdr -infiles single_subj_T1.nii single_subj_T1_original.nii
name offset nvals values
------------------- ------ ----- ------
pixdim 76 8 -1.0 1.8 1.8 1.8 0.0 0.0 0.0 0.0
pixdim 76 8 -1.0 2.0 2.0 2.0 0.0 0.0 0.0 0.0
qoffset_x 268 1 81.0
qoffset_x 268 1 90.0
qoffset_y 272 1 -113.400002
qoffset_y 272 1 -126.0
qoffset_z 276 1 -64.800003
qoffset_z 276 1 -72.0
srow_x 280 4 -1.8 0.0 0.0 81.0
srow_x 280 4 -2.0 0.0 0.0 90.0
srow_y 296 4 0.0 1.8 0.0 -113.400002
srow_y 296 4 0.0 2.0 0.0 -126.0
srow_z 312 4 0.0 0.0 1.8 -64.800003
srow_z 312 4 0.0 0.0 2.0 -72.0
Since the voxel size has changed, volumetry measurements in native space are affected and there doesn't appear to be a way to separate the original voxel dimensions (for volumetry) from the voxel to template mapping (when this mapping is 9 dof rather than 6).
thanks for your comments,
Jon
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