Dear Rosalia,
You definitely need to take lesions into account, and you will need to make
manual lesion masks. Mixing SPM and FSL is also going to make this a lot
more difficult.
We are working on a more automated approach to incorporating lesions
with VBM and so one option is to wait for the next FSL release (sometime
later this year). Alternatively, if you are already using SPM then it might
be easier to stick with that.
All the best,
Mark
On 3 Jan 2012, at 10:50, Rosalia Dacosta wrote:
> Dear FSL experts,
>
> I am trying to do VBM in order to test whether differences between my two groups in resting state might be explained by MRI-detectable loss of gray matter between these two groups.
>
> The big problem for doing this is that I have lesioned brains...and I don't know if it is possible to run BET and then use FSL’s VBM toolbox without mapping the lesions first.
>
> I have found that some authors use MRIcron for lesion mapping with T2, DWI or Flair images (hand made....I am unsure about the reliability of this method) and then coregister these images: realigment with T1 and normalization in a standard espace with SPM...
>
> Could you give some helping with this?
>
> Could I use normalized images from SPM (nii.gz) for FSL’s VBM toolbox to test the differences?
>
> Many thanks,
>
> Rosalia.
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