Brian,
OK. Does one specify the model with the -m flag in addition to the -intref
option? In essence, what is correct the command line format when
using -intref?
What do you mean by "leave-one-out cross-validation "
Thx...........J
----- Original Message -----
From: "Brian Patenaude" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Tuesday, July 08, 2008 8:13 PM
Subject: Re: [FSL] FIRST Hippocampus Segmentation
> 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
>>>>
>>
>
