Hi, in general it's a really bad idea to throw away resolution by
downsampling. In fact, you can get really nice results with BET just by
using the options -f 0.63 -c 75 123 166
You can get these options into the sienax script by taking a local copy of
$FSLDIR/bin/sienax and changing the bet line to:
${FSLDIR}/bin/bet $I ${I}_brain -s -f 0.63 -c 75 123 166 >> ${I}.sienax
Cheers, Steve.
On Mon, 19 Dec 2005, Gouw, A.A. wrote:
> Hi Steve,
>
> I have uploaded an example of a preprocessed scan (CP01_SIENAX_Gouw). the
> upload ID is 462510.
>
> Originally it was a sagittal MPRAGE(CP01_MPR), which was reoriented
> (reorient_CP01_MPR), then downsampled (reorient_CP01_MPR_reduced), then the
> neck was cut-off (xreorient_CP01_MPR_reduced), then BET with -f 0.45 -g -0.2
> (xreorient_CP01_MPR_reduced_brain, eyes and some skull is left, however some
> cortex was cut-off in the right parietal lobe), then sienax without BET.
> It seems that the segmentation was not correct in especially the temporal
> lobes (while the temporal lobes of the brain extracted image looks alright).
> So we think this might be a bias field problem.
>
> Do you have any suggestions?
>
> Thanks a lot!
> Best regards, Alida
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On
> Behalf Of Stephen Smith
> Sent: vrijdag 16 december 2005 16:24
> To: [log in to unmask]
> Subject: Re: [FSL] SIENAX 3D
>
>
> Hi - it't not very clear from the JPGs that you sent what's going on;
> mostly the image looks like the -f threshold should be lowered. In general
> we would not recommend downsampling the data. If you would like to upload
> an example original image we can have a quick look.
>
> Please upload the files in a single compressed tarfile to
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> and then email me the upload ID.
>
> Cheers, Steve.
>
>
> On Fri, 16 Dec 2005, A Gouw wrote:
>
> > Dear all, we are trying to run SIENAX on T1-3D images (1x1x1mm) in a
> multi-center setting. However, we've run into several
> > problems. We hope that you could help us out. First, BET does not give
> satisfying results. Even after changing the options -f, -g
> > and -c and cutting off the neck, manual editing is still necessary (parts
> of the eyes and skull). We think that it could be caused
> > by a wrong scanning angle. Therefore, while manual editing is not feasible
> on 256 slices, we downsample the images to 4mm slices
> > before running BET. Then we combine the manual and automatic masks and run
> SIENAX without BET. For some centers, this works out
> > well. For other centers however, BET and segmentation still give bad
> results. For sagittal MPRAGES the temporal regions are not
> > properly segmented (see fig 1), and for coronal MPRAGES this is the case
> in the frontal and occipital regions. We believe that it
> > is a bias field problem, and we are trying to solve it with optimal
> N3-inhomogeneity correction. However, this has not been
> > satisfactory yet. Do you have any suggestions, or have suggestions using
> different FAST-options? Another problem is that for some
> > centres the FOV is too small and some parts of the skull are not included
> in the image. Therefore the skull image is distorted (see
> > fig 2 and 3). Do you have any ideas of how to solve this? Thank you in
> advance, best regards, Alida Gouw A.A. Gouw, MD VU Medical
> > Centre Amsterdam The Netherlands
> >
>
>
--
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, 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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