hi Jong,
the -f option is to change the brain-extraction so will not directly
affect the segmentation of the brain into grey/white/csf. was the brain
matter unusally dark / lots of bias field? if you want to adjust "fast"
options you can add them to the end of the sienax command (type "fast" to
get usage details). the resolution etc can affect results quality, but in
general should not cause gross problems.
there should be almost no difference on different operating systems or
hardware - if you suspect there is a problem with one of your computers
you should run the FEEDS test on both.
regards, Steve
On Mon, 23 Feb 2004, Jong Chul Youn wrote:
> Hi.
>
> I'm using SIENAX for studying cortical atrophy in Alzheimer's disease.
> After getting my preliminary data, I wonder something like these.
>
> 1. During the reveiw of results using FSL view, I found some segmentation
> is incorrect. Some brain parenchyme is classified as CSF. How can I fix
> it? I think -f option can be used for this purpose. Is it right? If so,
> how can I find optimal threshold? Which anantomical structures should be
> reviewed? Can different values of FOV, matrix, slice numbers cause this
> problems?
>
> 2. How about different operating system? I analyzed my datas using both
> Redhat linux 7.x and 9.0,separately. I found results of brain volumes were
> not same. Is this natural? why did these results occured?
>
> (Sequence of MRI data are like this: T1/T2/FOV/matrix=14.4/5.5/20-
> 21/256*256 or 256*192)
>
> Best regards.
>
> Jong Chul, Youn M.D.
> Kunggi Provincial Hospital for the Elderly
> Repulic of Korea.
> e-mail: [log in to unmask]
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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