Dear Victor,
Sienax reports both normalised and unnormalised volumes.
The normalised ones are the ones transformed into standard (MNI) space and the unnormalised ones are in the native space. So just use the latter.
All the best,
Mark
On 20 Nov 2012, at 19:35, Victor DelBene <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I have completed preliminary volumetric analysis for three groups (2 clinical and 1 control) using FIRST. Images are 2x2x2 mm and were left in native space to remove the possibility of ROI warping or alterations if we performed a TAL or MNI transformation. We decided that volumetric and voxel values would be more accurate this way.
>
> Now, I am interested in finding out whole brain volume, CSF volume, and gray matter volume in these groups. I looked into Sienax, but found that this applies an affine transformation to MNI space. Is there a way to obtain these values without placing the brains into MNI space (ie. keep it in native space)?
>
> Thank you for the help!
>
> Victor DelBene
>
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