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>
>
> 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,
Gemma


>
>
>
> 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.
>>>
>>> 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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-- 
Gemma C. Monté Rubio
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