On 21 June 2012 17:40, Christopher Bell <[log in to unmask]> wrote:
> What do people think about using FAST segmentations to get an estimate of
> ICV? As long as you
> get good segmentations wouldn't atrophy just result in an increase in CSF
> and a corresponding decrease in WM and/or GM?
The problem is brain extraction. You could run FAST on an unextracted
head image -- this would take a long time, of course, and atypical
intensities outside the head could distort or invalidate the result.
You'd still have the problem of where to draw the boundary between
intra- and extracranial.
In principle, you are right, though. If you have a brain label from
somewhere (GM + WM), this can be extended into a reasonable estimate
of ICV: apply a Gaussian blur with a sigma of 6mm, threshold at 27%,
use FAST to label CSF within the resulting "dilated" mask, add that
CSF to the brain label, fill any holes. This achieves a fairly
consistent ICV estimate across normals and Alzheimer subjects
(Heckemann et al., Neuroimage 2011, Figure 5). It can still
underestimate ICV if there is very severe atrophy.
You would probably achieve the best possible result if you had a
library of manual ICV delineations on a set of MRIs that are
reasonably similar to your target image. Then you use a multi-atlas
label propagation and fusion approach to transform them into a target
ICV label. This is (in a nutshell) how "pincram" works, which is
currently ranked #2 behind the gold-standard labels on the
Segmentation Validation Engine (http://sve.loni.ucla.edu/archive/).
Regards
Rolf
>
> Chris Bell
>
> On Thu, Jun 21, 2012 at 1:13 AM, Mark Jenkinson <[log in to unmask]> wrote:
>>
>> Dear Gabor,
>>
>> Given the accuracy in calculating the ICV using SIENAX I think it is fine
>> to use this value and scale it to give you ICV.
>> If you have a very good brain extraction then FAST can give you a good TBV
>> (which is obviously not exactly the same as ICV, but for most purposes can
>> be substituted fine). It is very sensitive to the quality of the brain
>> extraction though.
>>
>> All the best,
>> Mark
>>
>>
>> On 21 Jun 2012, at 06:38, Gabor Perlaki wrote:
>>
>> > I need the TIVs because I want to report them. I know that correction
>> > with the TIV and correction with the scaling factor are identical, however
>> > if I'd like to report TIVs I need them. I think the TBV from FAST is not the
>> > best for this purpose, because using TBV as correction for head size may
>> > miss a global brain atrophy. Does anyone know how to calculate the ICVs from
>> > scaling factors? Can I use the volume of 1847712 mm^3 as the ICV of MNI152
>> > for this purpose, or do I need to recalculate it somehow? Or, any other
>> > method?
>> >
>> > Thanks,
>> > Gabor
>> >
>> >
>> >
>> >> You need to control for each individual subject's total brain volume.
>> >> It wouldnt make sense to regress out the volume of MNI template, since the
>> >> value of the covariate is >identical across subjects and contributes
>> >> equally to the dependent measure. FAST should output a TBV.
>> >> Good luck.
>> >> Christine
>> >
>
>
--
Rolf A Heckemann, MD PhD
Médecin chercheur, Fondation Neurodis
CERMEP - Imagerie du Vivant
Hôpital Neurologique Pierre Wertheimer
59 Boulevard Pinel
69003 Lyon
France
2nd affiliation: Honorary Fellow, Imperial College London
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