Hi,
The crucial thing here is to *look* at your results and decide which are better on the basis of better alignment in the registrations and more accurate segmentation of grey matter and white matter. Once you've decided which one is sufficiently accurate then use the results from that method. It sounds like at least one method is giving poor results, but it is impossible to say which one a-priori. If neither show registrations and segmentations of sufficient quality then you need to solve that before using any of these output values.
All the best,
Mark
On 12 Mar 2013, at 18:39, Estephan Moana <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I ran structural analysis on T1-weighted images of 2 groups (pain x controls) using both fsl_anat pipeline and SIENAX. When looking at the output, I saw considerable differences in what should be similar measures, for example:
>
> - Brain volume (normalized & unnormalised): fsl_anat = from output file "T1_vols.txt"; SIENAX = from output file "report.sienax"
> - Total grey & white matter volume: fsl_anat = followed FAST user guide steps for tissue volume quantification using partial volumes estimates; SIENAX = from output file "report.sienax"
>
> Are the above steps correct to extract those measures from fsl_anat and SIENAX output? Any ideas why these 2 pipelines are showing different results for similar measures? If these differences are to be expected, which pipeline you advise me to use?
>
> Thank you.
>
> Estephan Moana, D.D.S., M.S.
> Ph.D. Candidate
> Clinical Fellow, Oral & Maxillofacial Pain Program
> Regional Center for Neurosensory Disorders
> UNC School of Dentistry
> [log in to unmask]
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