I think this picture (attached) shows what's going on better than I can describe it. Note than I don't have whole brain coverage, so you're looking at a slab. In both examples of normalisation, template 6 and the flow-fields were generated previously when using DARTEL to normalise the functional and structural images for these same subjects.
Many thanks,
B.
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: 05 June 2013 22:37
To: Lawson, Rebecca
Cc: [log in to unmask]
Subject: Re: [SPM] Dartel normalise contrast mask
In general, it is safest to use the same (or similar) preprocessing for all your subjects. Whether you do the GLM after or before spatially normalising should not really make a large difference.
There will be a small discrepancy due to the REML estimation of the temporal correlations, but the thing causing the main difference will be the behaviour of the masking.
The easiest thing would be to use the "Run Dartel (existing template)"
option (using the previously computed Template data from the other
subjects) on the additional subjects, followed by the Normalise to MNI space option, and then the first level analysis to get the contrast images.
Generally, the flowery/swirly artifacts from normalising to MNI space will occur for regions of the head where no data was available in the original scans.
Best regards,
-John
On 5 June 2013 19:00, Lawson, Rebecca <[log in to unmask]> wrote:
> Hello,
>
>
>
> I've used Dartel to normalise some functional images and then taken
> these to first level analysis, then smoothed the contrast images and
> taken them to second level analysis. So long as I set the following during smoothing :
> matlabbatch{1}.spm.spatial.smooth.im = 1;%set mask to 1 to avoid crazy
> mask my second level mask looks normal.
>
>
>
> I now have a new first level analysis conducted in native space. I am
> attempting to normalise and then smooth the 1st level contrast images
> using Dartel. I have tried both the 'normalise2mni' routine and also
> the 'combine deformations' route (followed by a separate smoothing
> step) to achieve the normalisation of these contrast images. In both
> cases the normalised contrasts (and hence the mask created at the
> second level) are massive! The voxels around the brain (that are NaN
> in the functional images) are all given numbers very close to zero,
> and hence appear grey right to the edge of the FOV. Using the
> 'normalise2mni' routine this inflation occurs in x, y and z planes.
> Using the 'combine deformations' route this inflation only occurs in the x plane (left to right).
>
>
>
> I have already searched the spm archive and this "greying" of the
> contrast image beyond the brain looks different to the "flowery"
> effects that other people have reported after normalising contrast images using Dartel.
>
>
>
> Any ideas folks?
>
>
>
> B.
>
>
>
> -------------------------------------------------------
>
> Dr Rebecca Lawson
>
> UCL Institute of Cognitive Neuroscience
>
> 17 Queen Square
>
> London
>
> WC1N 3AR
>
>
|