Hi,
In a previous email I said that you can reslice to axial using
fslswapdim
and gave the example commands:
imcp N06 N06_orig
fslswapdim N06 RL PA IS N06
You should then view the image in FSLView, find the lowest slice
that you wish to include and how many slices you need to include
to cover the brain (subtract the lowest one from the highest one
that you want included) and then do:
fslroi N06 N06_cropped 0 160 0 256 A B
where A is the lowest slice number and B is the number of slices
to keep. For example, on E05 I did:
fslroi E05 E05_cropped 0 160 0 256 57 150
(as slice 57 was just underneath the cerebellum and slice 207
was just above the head).
You should then look at the image again in FSLView to check that
it has done what you want.
I gave you the exact command that you need to run for sienax.
There is nothing more, although you may need to try different
options for BET - please read the documentation on BET to see
what is available.
Once sienax has finished just look at the results.html file in a web-
browser
to see the output images and check these for quality of the brain
extraction and registration. If they are fine then you can look at
the contents of the report.sienax file (which is plain text) and find
the line that defines VSCALING.
All the best,
Mark
On 10 Nov 2009, at 12:20, SUBSCRIBE FSL hankee wrote:
> Hi, FSL experts.
>
> After reading the answer, I am still very confused,maybe I am too
> dull.
> I haven't know how to reslice to axial and cropping with FSLROI
> command?
> and I am not very familiar with SIENAX command. So can you list the
> steps
> about how to measuring the ICV procedure and give some discription?
> Thank you very much!!!
>
> yours sincerely:
> Hankee
>
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