Hi,
There are 2 different models for the hippocampus, caudate, and
amygdala. The shape model portions are identical, the differences are
in the intensity model, more precisely, in its normalization. The
models that are located in ${FSLDIR}/data/first/models_317_bin/ are
all normalized by subtracting the mode of the intensity distribution
within that structure. When fitting the model, this normalization
constant is estimated from the data.
The problem with the 3 structures mentioned above is that in the case
of severe atrophy, the initial structure estimate may encompass a
significant amount of CSF, thereby confounding the normalization
constant estimate. To get around this, models have been created that
are normalized by the mode of the intensity distribution of the
thalamus (which is more robustly estimated).
Based on leave-one-out cross-validation using the intensity reference
models perform, on average, slightly better.
The general recommendation for the hippocampus is to use the
intensity reference model (in ${FSLDIR}/data/first/models_317_bin/
intref_thal ) with 30 modes of variation (this is what is done in
run_first_all).
For the example image you provided, it is seems to do better in
capturing the lateral portion of the body of the hippocampus (though
a few voxels may still be missing). Similar results can be obtain for
the standard model if you increase the number of modes to 60 or a bit
above.
Hope this helps and clarifies things.
cheers,
Brian
On 7 Jul 2008, at 14:10, Jay Ives wrote:
> Hi Brian,
>
> Thanks for your interest. The files are ROA.hdr and ROA.img. The
> upload session reference number is 994681.
> I converted the DICOM image set to ANALYZE format with MRIConvert
> so as to use MRIcro to clip and convert to axial format to use in
> FIRST.
> I find the lateral aspect of the left hippocampus body is not
> completely within the model. I don't think there is anything else
> there such as choroid plexus.
> I look forward to your comments.
>
> Cheers................J
>
> ----- Original Message ----- From: "Brian Patenaude"
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Monday, July 07, 2008 5:59 PM
> Subject: Re: [FSL] FIRST Hippocampus Segmentation
>
>
>> Hi,
>>
>> Could you upload an example image at http://www.fmrib.ox.ac.uk/
>> cgi- bin/upload.cgi ?
>>
>> Cheers,
>>
>> Brian
>>
>>
>>
>>
>> On 6 Jul 2008, at 13:59, Jay Ives wrote:
>>
>>> The lateral aspect of the hippocampus body is occasionally not
>>> included
>>> within the surface. I've tried 30 and 40 modes and different p
>>> values in
>>> these cases, but without effect. Is there anything else that can
>>> be tried?
>>> Thx....J
>>>
>
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