on the same topic:
I don't understand why DARTEL is initialized only with the rigid component of the matrix stored in the _sn.mat and not with the affine transformation.
Could you clarify this point?

From some notes by John Ashburner, the idea is to do all the nonlinear warping with the DARTEL algorithm, so that all shape parameters are estimated in a similar way with the DARTEL algorithm. This is rather tidier, especially if the idea is then to analyze shapes using the DARTEL "flow fields".

Best regards,

Quoting "MCLAREN, Donald" <[log in to unmask]>:

(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.


Neil Chatterjee
Research Assistant
Stanford Systems Neuroscience and Pain Lab
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Best Regards, Donald McLaren
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
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