Hi,
On 1 Feb 2007, at 15:58, Bum Seok Jeong wrote:
> Hi,
>
> In my case, neck area is always remained after BET during SIENA.
> If I have segmented brain (WM, CSF, GM), is there any way to bypass
> only the segmentation process of SIENA?
Well, you could edit $FSLDIR/src/siena/siena_diff.cc and change
if(1) // always done unless the above uncommented and used instead of
this test
to
if(0)
and it will use the pre-existing segmentations
> In my knowledge, SIENA is a tool to compare between two time point
> in same subject.
> Is it possible to compare among three time point in same subjects
> like repeated measure anova?
SIENA can only take in two images, but you can run all 3 pairings and
combine the results in a number of statistical ways.
You might look at Frost et al Statist. Med. 2004; 23:3275–3286
Cheers, Steve.
>
> Bests,
>
> bsjeong
>
>
>
> Steve Smith wrote:
>> Hi,
>>
>> At this point SIENAX does not use betsurf to generate the skull
>> outline, it uses the simpler skull output by bet itself. Hence the
>> brain extraction and the skull estimation are both estimated at
>> the same time by the same call to bet at the start of SIENAX.
>> Hence whilst it is easy to change SIENAX to allow you to hand edit
>> the brain extraction, it's not so easy to feed that hand editing
>> into the skull estimation.
>>
>> However, I'd be surprised if this made much difference anyway -
>> the bet skull estimation has always been quite rough, but that is
>> fine for the purposes of fixing the scaling constraint in SIENAX.
>> If you use the -d option in SIENAX you can check the intermediate
>> stages, but it's probably working fine.
>>
>> Cheers, Steve.
>>
>>
>> On 1 Feb 2007, at 00:23, Russell Chu wrote:
>>
>>> Hi All,
>>> Currently, I'm using BET to generate a brain mask, which I hand-
>>> edit and use
>>> to extract the brain from T1-weighted MR images. Just by visual
>>> inspection,
>>> it seems that brain masks requiring significant hand-editing also
>>> have less
>>> accurate skull outlines generated with BETSURF. If this is the
>>> case, then
>>> less accurate inner skull outlines may adversely affect the inverse
>>> v-scaling values from SIENAX. Would it be possible to somehow take
>>> advantage of the hand-edited masks by inputting them into SIENAX
>>> to improve
>>> the inverse v-scaling value? Any input would be greatly appreciated.
>>> Thanks in advance.
>>>
>>> Cheers,
>>> Russell Chu
>>
>>
>> ---------------------------------------------------------------------
>> ------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------
>> ------
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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