segmentation of brain from CT

Hi,
I am just trying to segment brain from CT. Is there a way to segment brain from CT data or it is possible to segment brain from only MRI. Anyone can help me with this issue.

Thanks in advance,
Suba

Do you mean you would like to remove the skull? Swiss Skull Stripper extension should be able to do that completely automatically. The built-in atlas is optimal for MRI, but if you segment a CT manually then you can use that as atlas and may get better results.

See for example the result it gave for the CTBrain sample data set:

image

Hi,

Thank you for your valuable reply.

I have attached the screen shot of the brain segmented from MRI. Will I be able to segment the brain with those grooves and more detail from CT data.

Thanks and regards,

Suba

You will not get the same level of detail from CT as from MRI - see below MRI and CT image of the same patient, showing the same image slice:

image

Hi andras,
Is it possible to get the brain portion automatically without the cerebellum part of the brain(the back lower brain portion)

thank you

Regards,
Saima Safdar

Contrast between cerebellum and other parts of the brain is not very good but you can try to modify the atlas that the skull stripper module uses and see if it can provide the region you need.

How can i modify the atlas. I do not understand this. Could you please tell me how can I change it.

You can import the atlas labelmap volume node into a segmentation node using Segmentations module, then edit it using Segment Editor module, finally export the segmentation to a labelmap volume node. See segmentation tutorials here.