Hi,

On 30 May 2007, at 03:23, ramya priya wrote:

> I have few questions regarding the calculation of brain volume
> using SIENAX.
>
> 1. Is there any difference in the brain volume between 2 sequences
> with and without any gap? Does SIENAX estimate the gap area into
> the total brain volume when there is gap between slices?

_Almost_ always in MRI analysis there is no need to differentiate
between imaging with and without gaps, as long as the total effective
slice thickness (including any gap) is correctly set in the header.
Programs like SIENAX will work fine as long as the image quality is ok.

> 2.If we have a T1 weighted sequence, slice with 6mm thickness and
> 1 mm gap,does it make a difference on the brain volume calculation?

The gap is not a problem - you have an effective slice thickness of
7mm and the header should show 7mm for pixdim3. However, unrelated to
the gap, 7mm is rather thick, so you will not get as accurate SIENAX
results as you would with thinner slices.

> 3. In our studies,we observed that few cases have bad results
> (brain vol less than 1200ml) even though the parameters of these
> cases are the same as other cases with good results(vol between
> 1300ml-1700ml)?what factors affect the calculation of the brain
> volume? Please let us know.

Probably just because your slices are rather thick....you should run
SIENAX with the -d option and look carefully at the different output
stages to check what's going on - for more hints on this, see the
segmentation lecture slides on the FSL course page.

Cheers.

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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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