(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.
(2) In theory, the c*.img will produce crisper segments after warping
because they have one less resampling step in the data processing stream. I
have not yet inspected the differences between using rc* and c* files, yet;
but it is on my to do list.

(3) Creating flow field steps should always use the rc* files.

On Fri, Jul 24, 2009 at 7:50 PM, Neil Chatterjee <[log in to unmask]> wrote:

> Dear SPMers,
> 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.
> Regards,
> Neil
> Neil Chatterjee
> Research Assistant
> Stanford Systems Neuroscience and Pain Lab
> [log in to unmask]

Best Regards, Donald McLaren
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Office: (608) 265-9672
Lab: (608) 256-1901 ext 12914
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