Hi,
On 29 Oct 2008, at 04:45, Anthony Ang wrote:
> Hi Steve,
>
> I think now I get a clearer picture.
>
> Please correct me if this is right: -
> The caudate, putamen, insula and thalamus in the thr0 version all
> are larger than the corresponding regions in the MNI152 brain - but
> this does not matter when you multiply their binary masks to the
> MNI152 brain segmented GM as the excess voxels will be removed.
>
> But the boundaries between the different lobes (parietal/occipital/
> temporal/frontal) and cerebellum are accurate - these lobes are only
> dilated/extended only in one direction towards the external non-
> brain space. This means that when the lobe binary masks are
> multiplied to the MNI152 brain segmented GM and WM, you will get the
> correct GM and WM for each lobe.
>
> The reason why I use MNI-maxprob-thr0-2mm atlas is because this
> atlas must be derived from MNI152_T1_2mm_brain image and I could
> use the MNI152_T1_2mm_brain image provided to fnirt/invwarp the
> MNI152 image to my subject image and from the transformation matrix
> obtained, I could warp the atlas to my subject image.
No, just use a summary image that is thresholded at a different cross-
subject-percentage level - such as MNI-maxprob-thr25-2mm or MNI-
maxprob-thr50-2mm - then none of the structures will be "too large".
> Is the Harvard-Oxford atlas (and other atlases) also based on the
> MNI152 brain?
Yes.
Cheers.
>
>
> Thank you very much.
>
> Best regards
> Anthony
>
>
>
> On Tue, Oct 28, 2008 at 6:22 PM, Steve Smith <[log in to unmask]>
> wrote:
> 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
>
>
>
>
>
>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
---------------------------------------------------------------------------
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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