(1) The rc*.nii images are rigidly aligned (6 parameters) to the MNI template space. This is done by applying the rigid component of the transformation stored in the *_sn.mat files.
I'm trying to understand the Initial Import step for DARTEL a little better, and I'm hoping someone here can help me out.
Compared to the gray matter from the segment algorithm (c1*.nii), the imported segments (rc1*.nii) seem to be aligned slightly differently (see attached "misalignment.png"). The DARTEL guide indicates that some sort or rigid tissue alignment is happening in the import step, so this isn't too surprising, though I am kind of lost as to what is being aligned to what. Are the tissue classes rigidly aligned to some sort of SPM template?
Referring to the imported images, the DARTEL guide also says that "the headers of these files encode two affine transform matrices, so DARTEL tools are still able to relate their orientations to those of the original T1-weighted images". Am I then correct in understanding that the flow fields map the transformation from the original space of the T1 images to the group template? To test it out, I warped a set of T1 scans before and after coregistration to the rc1*.nii images (see "avg_anat.png" attached) using flow fields (u_rc1*.nii) from the dartel imported GM segments (rc1*.nii). anat.nii shows the mean of the warped original T1 images, and ranat.nii shows the mean of T1 images that had been coregistered to the rc1*.nii images prior to warping (rc1*.nii = ref, c1*.nii = source, T1 = other) . anat.nii looks much cleaner than ranat.nii, implying that flow fields map from original space to group template space.
Am I to take it then, that when creating modulated GM segments for t-tests, I should use the original segments and NOT the segments from DARTEL's initial import? Comparing averages of warped GM segments from before (c1*.nii) and after (rc1*.nii) import, it looks like it's the c1*.nii that warp together better (see attached "avggray.png"). If so, then perhaps there is a slight mistake in the DARTEL guide, which indicates that the rc1*.nii files (not the c1*.nii) should be selected when running "Create Warped". Or is it that "Create Warped" and the Deformations toolbox are not doing the same thing?
Any clarification would be much appreciated. This is using an updated SPM8 on Matlab 2008b.
Stanford Systems Neuroscience and Pain Lab
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