Dear Noelia,
there is a batch function in CAT12 that applies your lesion mask to your T1 data:
SPM->Tools->CAT12-Tool->Manual image (lesion) masking
However, keep in mind that the stroke lesion processing is still experimental and if lesions are too large this will also impact preprocessing quality.
Best,
Christian
On Thu, 5 Sep 2019 08:44:13 +0100, Noelia Martinez Molina <[log in to unmask]> wrote:
>Dear CAT12 experts,
>
>I´d like to run a VBM analysis with stroke patients using the stroke lesion correction in cat12 expert mode. Basically, I´d like to set the intensity of voxels inside the lesion to 0 to avoid normalization of the lesion.
>
>I then chose manual SL handling in the Stroke Lesion Correction option. My question is: where do I include the binary lesion mask as input? Or do I have to multiply the T1 by the lesion mask to set these voxels to 0 intensity?
>
>Thank you in advance for your assistance!
>
>Best wishes,
>Noelia
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