Hi,
The following information on obtaining volume measurements from FAST
should help.
The best estimate of volume for any of the segmented matter types is
obtained by summing up the partial volume estimates (PVE) which should
be saved as separate outputs using the -e and -ov options. To obtain
the sum, the easiest way is to use avwstats to get the mean value and
the total volume - the product of these values is then equal to the
desired volume. For example, if mybrain_pve_0 is the output
corresponding to the CSF segmentation, then the avwstats calls are:
avwstats mybrain_pve_0 -m
avwstats mybrain_pve_0 -v
The resulting mean value from the first call should then be multiplied
by the first output of the second call to get the volume in voxels, or
by the second output of the second call to get the volume in mm^3.
Note that to get a good estimate of intracranial CSF volume it is
necessary to use an input image to FAST that has good contrast between
CSF and skull. A T2-weighted image is suitable for this, but a normal
T1-weighted image is not.
Whether you will get more accurate measurements from your T2 or SPGR
sequence will depend not only on the resolution but on the tissue
contrast.
Hope this helps.
All the best,
Mark
On Monday, January 12, 2004, at 06:49 am, Jong Chul Youn wrote:
> Hi.
>
> I have 3D SPGR(1.5 mm thickness) and T2 axial(5 mm thickness and 1.5 mm
> gap) MRI data.
> And, I want to get intracranial volume using FSL software for
> normalization of hippocampal volume.
> How can it possible?
>
> (In my opinion, two ways are possible
>
> 1. segmentation of T2 axial data using FAST
> 2. registation of T2 to SPGR using FLIRT and FAST
>
> Is it possible and can get correct results?)
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