Hi,
OK, this VSCALING seems more sensible.
If you are happy with the brain extraction and
registration in the output then this is all you need.
Just multiply the volumes you get from FIRST
with VSCALING to get the normalised volumes.
The output for BRAIN gives you the volume of
the brain *not* the intra-cranial volume. However,
the VSCALING gives you the factor that you need
to apply to make the intra-cranial volume consistent
(that is, normalised) for all subjects. It scales
everything by the factor required to make the
intra-cranial volume of this subject equal to the
intra-cranial volume of the standard-space template
So all you need to do is just multiply any volume
by VSCALING to get the normalised volume (which
is equivalent to normalising by the intra-cranial volume).
I hope this is clear.
All the best,
Mark
On 11 Nov 2009, at 04:16, SUBSCRIBE FSL hankee wrote:
> Hi, FSL experts,
> Thank you for all your help! Now I do follow the following steps as
> you tell me:
> 1.imcp N06 N06_orig
> 2. fslswapdim N06 RL PA IS N06
> 3.fslroi N06 N06_cropped 0 160 0 256 52 190
> then chek the image using the fslview, very good! So I run the step 4
> 4.sienax N06_cropped.nii.gz -o N06_sienax -B "-f 0.3 -R"
> When this command is done, I see the report.html file and find the
> segment
> is very good. So I open the report.sienax file, just as below:
>
> SENA - Structural Image Evaluation, using Normalisation, of Atrophy
> part of FSL www.fmrib.ox.ac.uk/fsl
> running cross-sectional atrophy measurement: sienax version 2.6
> sienax
>
> ---------- extract brain
> --------------------------------------------
>
> ---------- register to standard space using brain and skull --------
> (do not worry about histogram warnings)
> VSCALING 1.2515755727
>
> ---------- mask with std mask
> ---------------------------------------
>
> ---------- segment tissue into types
> --------------------------------
>
> ---------- convert brain volume into normalised volume
> --------------
>
> tissue volume unnormalised-volume
> GREY 798467.69 637970.02
> WHITE 703811.83 562340.65
> BRAIN 1502279.52 1200310.67
>
> So the 1502279.52 is N06's intracranial volume? Is that right?
>
> the way, Whether left Hippocampus volume which produced by FIRST
> tool also
> need VSCALING to normalise before the statistic analysis?
>
> Thank you very much!!!
> Best regards!
>
> your sincerely:
> Hankee
>
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