Hi,
NO! the atlas is already in the correct space of the MNI152 - it's
just dilated because you're looking at the thr0 version. You can get
exactly what you want (more 'average' masks by either using one of the
more sensible thresholding images (thr25 or thr50) or just by taking
the full unthresholded 4D probability images and thresholding them
yourself - but that shouldn't be necessary. In general however I might
recommend using the Harvard-Oxford atlases instead as these have more
detail in them.
Cheers.
On 28 Oct 2008, at 05:36, Anthony Ang wrote:
> Dear Steve,
>
> Thanks for your reply.
>
>
> On Sat, Oct 25, 2008 at 12:11 AM, Steve Smith <[log in to unmask]>
> wrote:
> Because the MNI152 is derived from a mixture of Americans and
> Canadians, whereas the probability masks are just Canadians, who
> have larger brains.
>
> This is very funny! Have a good laugh.
>
>
> Oh, my wife tells me that's not the case, so it must be: the
> MNI152_T1_1mm_brain is the result of averaging together many brains,
> and so reflects the average size, whereas the MNI-maxprob-thr0-1mm
> by definition is the multiple-subject atlas data thresholded at
> "thr0" - so by definition it will reflect the largest brains used
> for the atlas, not the average. You can ignore the extra voxels if
> you're only interested in results inside the average brain.
>
>
> Can I crop away the excess mask (not covering the brain)?
>
> Yes.
>
> If I just crop away the excess mask, I find that most of the masks
> (e.g. caudate Intensity value 1, putamen Intensity value 7 and so
> on) are actually larger than the corresponding regions/lobes on the
> MNI152_T_1mm_brain image.
>
> I carried out a flirt ( MNI-maxprob-thr0-1mm to MNI152_T1_1mm_brain)
> which improves the correspondence a bit but the edges/boundaries of
> each lobe/region in the output image are not correct. For example,
> the parietal lobe (intensity 6) have bits of intensity 1, 4 and 5
> around it, which means that when I create masks of lobes from the
> flirted-MNI-maxprob-thr0-1mm by intensity thresholding, these masks
> will not be accurate.
>
> What are your suggestions that I should do? Are there any other
> better masks of brain lobes that I can use?
>
> Thank you very much.
>
> Best regards
> Anthony
>
>
>
>
>
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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