Thanks, I will let you know how it works out. Stefano
-----Original Message-----
From: Stephen Smith [mailto:[log in to unmask]]
Sent: Tuesday, November 27, 2001 12:42 PM
To: [log in to unmask]
Subject: Re: [FSL] segmentation problems
Hi - thanks for your email.
1) the first thing to try is the latest version of FAST - take
http://www.fmrib.ox.ac.uk/~steve/ftp/fastlinux.tar.gz and put the binaries
in fsl/bin (make sure they are executable) if you are not using linux,
let me know which platform you need binaries for and I can send them to
you. if this does not fix your problem, email me directly with the images
and we'll look at them.
2) you can setup a raw text file with mean intensity values (separated by
newlines) for the starting mean values of the different classes to be
segmented.
hope this helps! :)
Stephen M. Smith
Head of Image Analysis, FMRIB
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
On Tue, 27 Nov 2001, Marenco, Stefano (NIMH) wrote:
> I think my email got rejected after trying to attach images in it.
>
> I am having trouble doing a segmentation starting from a brain extracted
> volume that I created in medx with FSL tools. The input image is a T1
> weighed SPGR. The output that was prescribed is a 3 classes image, with
all
> classes in one image. The result is a brain that looks like a mask with
> mostly matter and some gray matter in the middle, a background that
> corresponds to the gray matter values and a rim around the head that looks
> like a skull with an inner rim of CSF values and an outer more narrow rim
of
> white matter values.
> 1) Has anyone encountered this before? and can anyone tell me how this
came
> about? I did several other similar segmentations without this problem.
> 2) If I want to use a file to prescribe beginning values for the
> segmentation compartments, which form should the file have?
> Thanks,
> Stefano Marenco, M.D.
> Senior Staff Fellow, NIMH, CBDB
> Bldg 10 room 4S235
> 9000 Rockville PIke
> Bethesda, MD 20892
> email: [log in to unmask]
> tel: (301) 435-8964
> fax: (301) 4807795
>
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