Dear Sebastian,
you can save label images in native space that provide mask information. These label images can be used to mask the coregistered Flair images using imcalc. If you select the label and the Flair image simply use "i1.*(i2>0)" to threshold the Flair image according to the label.
Regards,
Christian
PS: If you are interested in detecting lesions in the Flair images you can also try the Lesion Segmentation Toolbox:
http://dbm.neuro.uni-jena.de/software/lst/
On Tue, 8 Jul 2014 10:03:32 +0100, Sebastian Papazoglou <[log in to unmask]> wrote:
>Dear SPMers
>
>Currently I am working on a set of T1 and Flair images. The Flair images have been coregistered to the T1 images. In a second step, the T1 images were warped to the Dartel template space using VBM8 write&estimate.
>Now, I would like to have skull-stripped Flair images warped into the same space. I could apply the deformation fields from the T1 warping (the y_*) to the Flair images using Apply Deformations (from the VBM8 tools) but they would not be skull-stripped then…. Is there a way in SPM to have the Flairs warped and skull-stripped?
>
>Many thanks!
>
>All the best,
>Sebastian
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