Hi - sorry you're having problems with your nose.
I recommend following the advice I sent yesterday - run BET, then run FAST
to get expanded bias field which you can then apply using avwmaths to the
original image to get a corrected image.... I wouldn't worry about your
nose if you go this route.
ttfn, Steve.
On Thu, 29 Aug 2002, Darren Weber wrote:
> Dear Steve, Mark, et al,
>
> T1 MRI of the whole head was acquired in the sagittal plane (0.98 x 0.98,
> 256 x 256) with 128 slices (1.3047 mm thick). The volumes are 16 bits.
>
> In some cases, the tip of the nose is located in the posterior coronal plane
> (an artifact of the reconstruction process). It is easy to relocate 10-20
> coronal slices to the anterior, effectively putting the nose back into its
> proper real world location (there is a clear gap between the nose and the
> back of the head).
>
> A couple of simple questions...
>
> Q1. Is it better to estimate and correct RF bias fields on the volume
> before or after relocating the nose?
>
> My guess would be that relocating the nose will lead to better RF bias field
> estimation, especially with FAST. I assume, with FAST, that the RF bias
> field estimation/correction is an integral part or product of the MRF
> calculations. Furthermore, I assume that the MRF and neighbourhood
> relationships can be calculated over the entire FOV of the volume, including
> all head and non-head voxels (which would include artifacts and noise). I
> presume that this information is then utilised for segmentation, that is,
> the MRF and neighbourhood information is a continuous 3D function that is
> generated and then utilised for refinement of segmentation into tissue
> classes. If the neighbourhood information is more consistent by putting the
> nose "back in place," this should result in better RF bias estimation.
>
> Q2. We're using some software that is sensitive to RF bias. All we need is
> an RF corrected volume, not the segmentation. Is it then reasonable to use
> FAST on the whole FOV of the volume, before BET, just to extract the RF bias
> corrected volume?
>
>
> Take care, Darren
>
>
> PS, all the best with the Oxford workshop.
>
>
> --
> Darren Weber, PhD Student
> Cognitive Neuroscience, School of Psychology
> Flinders University of SA, GPO Box 2100, Adelaide, SA 5001, Aust.
> Ph: (61 8) 8201 3889, Fax: (61 8) 8201 3877
> http://203.3.164.46/~dlw/homepages/index.html
>
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
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