Dear Shi,
The b0 image acquired without any diffusion weighting gives higher
signal-to-noise ratio than DW images, you might notice when looking at
the images that the contrast is also way better in the b0 image.
Also the b0 image will suffer from fewer artifacts than the DW images,
this is why we use it as a reference volume during registration.
The b0 image is not chosen as a mask, a mask can be generated from it
easily because of the contrast as I said above. So that you can avoid
doing unnecessary computations around the brain.
However, b0 images can be distorted in readout-direction, these are
called EPI distortions, you might correct these by acquiring a field map
or a structural scan (preferably T2 image because of similar contrast
and intensities) for non-linear coregistration.
Hope it helps.
All the best,
Barbara
On 28/06/2014 08:18, SUBSCRIBE FSL Xinfa_Shi wrote:
> Hi ,
>
> I am running through the TBSS processing stream .When creating FA images from your diffusion study data ,a step is to create a brain mask by running bet on one of the B=0 (no diffusion weighting) images . I use the command "fslroi data nodif 0 1 " to extract b=0 image .
>
> As far as I know , b=0 image is used as mask when extracting brain .Could you explain it ? Why is b=0 image chose as mask ? How does it works? What's is its function ?
>
> Regards .
>
> Shi Xin-Fa.
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