Dear Stefano,
In answer to some of your questions...
> When I use sinc interpolation, which filter should I use and what size?
> I used Haninng 7 voxels for registering the images prior to segmentation,
> how does that sound (there must be a reason why it's default) ?
There is no general concensus on what interpolation gives the best results.
We left 7 voxel Hanning as the default as it gave good results in a
reasonable time. But the only way to really know if other kernels might
be better is to try them. However, my suspicion is that it won't be
that significant - there isn't anywhere near as much difference as there
would be between sinc and trilinear.
> The other question is where are the transform files saved after
> registration? In the GUI I see no option to save the transform files, yet I
> imagine that the .mat files that are created may be the xform. Can I take
Yes, that's right. The .mat files are the transformation files that
flirt saves. They are in ascii format (not MATLAB) and can be viewed
as text files (a 4x4 affine matrix). However, they are not MEDx transforms
and so if you want a MEDx transform then you should use the save shadow
transform option immediately after getting the transformed image.
An alternative is to use the command line program "convert_xfm" to
convert the .mat file into a MEDx .xfm file.
> these files and shadow-transform other volumes? How do I do that?
Once you have the .xfm MEDx version you can happily shadow-transform away
as normal.
Note: If you want to use it outside of MEDx then you need to
use the -init and -applyxfm options to the flirt command line program.
> What are MRF's?
Markov Random Fields.
They are a mathematical form for imposing neighbourhood relations between
the probabilities that helps to do spatial regularisation (like smoothing)
to the internal segmentation-finding parts of FAST.
Cheers,
Mark
> -----Original Message-----
> From: Stephen Smith [mailto:[log in to unmask]]
> Sent: Wednesday, January 16, 2002 5:20 PM
> To: [log in to unmask]
> Subject: Re: [FSL]
>
> Hi
>
> On Tue, 15 Jan 2002, Marenco, Stefano (NIMH) wrote:
>
> > Is there any particular order I should apply susan and brain extraction?
> > I seem to get different results when I invert the order of these
> operations.
> > Is this to be expected?
> > And what does susan actually do?
>
> They are both nonlinear processes so yes, the order will affect things.
>
> You should not normally need to apply susan before BET. In general, we do
> not use SUSAN before our other programs as they are all designed to be
> robust. For example, the FAST segmentation effectively includes its own
> "spatial regularisation" (MRFs on the class labels), so SUSAN is
> definitely not recommended in that case.
>
> SUSAN is a nonlinear noise reduction algorithm - see
> http://www.fmrib.ox.ac.uk/~steve/susan
>
> ttfn :)
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