SPM won't deal with the cyst very well as all brain tissue is classed
as either GM or WM. You could manually segment the cyst and provide a
mask to the segmentation so that it ignores that part of the image.
This would give you GM and WM. You'd then need to combine the manual
and automated segmentations (eg with ImCalc) to obtain the three
classes you want.
Best regards,
-John
On 15 May 2012 14:23, Istace, Audrey <[log in to unmask]> wrote:
>
> Hi SPM experts,
>
> First I would like to thank you for your answers to my previous question : I
> am now able to use SPM without Matlab (with SPM standalone).
>
> However, I have another question about the segmentation : I would like to
> classify a MRI into white matter, grey matter and csf. I was able to
> reorient my images for them to correspond to the atlases, but I am wondering
> if I should make some preprocessing before using the module "Segment". For
> example, should I use "Realign" or "Coregister", or something else, in order
> to get the better classification as possible?
>
> Another question I have about segmentation is the following one : does the
> algorithm of segmentation calculate the intra cranial cavity in some step?
>
> Thank you very much.
>
> Best regards,
>
> Audrey
>
>
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