Hi Sam,
That sounds a bit unintuitve indeed. Both methods word quite differently though, so they will not necessarily produce the same result. FAST (used by fsl_anat) classifies each voxel in the brain as either grey or white matter (or CSF) based on its intensity, which works very well for the cortex. It is not the optimal way to segment the subcortical structures however, as the image intensities in the different structures are not described very well by the simple choice between grey and white. FIRST takes more knowledge of the structures to be segmented into account and estimates the size and shape of the structures, rather than classifying the individual voxels. This should normally yield much more accurate segmentations.
If you want to investigate this further, I would suggest having a look at the gray matter volumes produced by fsl_anat (…_pve_1.nii.gz). It is also in general a good idea to carefully check the segmentations produced by FIRST.
Cheers,
Eelke
> On 13 Mar 2015, at 16:08, Sam Rogers <[log in to unmask]> wrote:
>
> Hi.
>
> I'm surprised to see that VBM suggests atrophy in subcortical regions, yet volumetric data from first suggests the opposite. I have used first implemented in fsl anat.
>
> Can anyone explain this please?
>
> Thanks.
>
> Sam.
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