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
Could you clarify this point?
Thanks for your help
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
>> [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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