Hi Steve,
I've tried the -B option inside siena ( -B "-B") though in this case
automatically i exclude bet_robust choice from siena. There's no way to feed
siena with the image that comes from betrobust segmentation of the
betpremasked image? I am asking that because when i applied betrobust on an
image which was first betpremasked i had excellent brain segmentation
results and i hope that the same would happen if i could manage to combine
both of the tools in siena
When i used -B "-B" option on siena even though the bet results were decent
(but definitely not as good as the results that i had using betrobust on the
betpremasked image) and i thought that my problem was solved, i noticed that
the halfway tranformations on both images were totally wrong containing all
the neck... why this happened since bet extraction was done successfully in
siena?What do you suggest to do in this case?
I've uploaded the png files that shows the different stages of siena (which
failed) on the A and B images with the ref number: 625404
Thanks again Steve
Antonios-Constantine Thanellas
On Thu, 25 Oct 2007 07:42:33 +0100, Steve Smith <[log in to unmask]> wrote:
>Have you tried the -B option to bet? You can pass that into SIENA by
>adding onto the end of the SIENA command
>-B "-B"
>Cheers.
>
>
>On 24 Oct 2007, at 20:52, Antonios - Constantine Thanellas wrote:
>
>> Dear fsl users
>>
>> I want to betpremask (through standard_space_roi) my data in order
>> to do
>> longitudinal and cross sectional analysis with siena and sienax
>> respectively.
>>
>> Since siena needs the skulls of the original images i can't just do
>> a shell
>> script that sends as inputs to siena the stripped brain images after
>> betpremasking them. I've read in FSL forum that it's better to
>> change the
>> siena script as follows: "leave BET to extract the skulls, then run
>> betpremask and feed, then run again bet on the premasked images and
>> feed
>> siena with these results." The problem is that siena script is too
>> complicated for my scripting skills and i would really appreciate
>> if you
>> could tell me how to change this script in order to betpremask my
>> data first
>> (bet_robust totally fails in most of my data which contain big
>> protions of
>> neck even if i determine the COG with the -c option.That's why i need
>> betpremask since it gives me really good results).I use the fsl 4.0
>> version
>> on ubuntu platform.
>>
>> How about sienax ? it also needs the skulls in order to register
>> the images
>> with pairreg? How the sienax script should be changed in order to
>> incorporate betpremasking?In this case also, a shell script that
>> sends as
>> inputs to sienax the betpremasked images wouldn't work..Right?
>>
>> Thank's a lot for your time
>>
>> Antonios-Constantine Thanellas
>
>
>------------------------------------------------------------------------
>---
>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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