Hi Krish - glad you're happy with this. You might want to add a note to
your new web page that the number of main iterations (-i option) and
smoothing of bias field (-l option) might need optimising for different
strong bias fields. For example, for one multi-channel surface coil I
ended up using "-l 200 -i 50".
On Wed, 2 Jun 2004, Dr Krish Singh wrote:
> Cheers Mark (and Clare),
> This appears to work *really* well on our Siemens Trio mp-rage images. Using
> the 8-channel head-coil we get really nice images but there is a noticeable
> brightening towards the back of the head. Fast gets rid of this (apparently)
> I've written some instructions (including an automating script) at the
> following webpage:
> Might be be useful for some people.
> Thanks again for another great tool!
> On 1/6/04 1:15 pm, "Mark Jenkinson" <[log in to unmask]> wrote:
> > Hi Krish,
> > The segmentation and bias field are all part of the same model
> > in FAST and so you cannot estimate one without the other.
> > When you turn on or off different outputs it doesn't change the
> > internal working, just what gets saved. So I'm afraid there's no
> > easy speed-up for you by this route.
> > Applying a bias field, however, is easy and yes, you just need
> > to use avwmaths. See the following page from the fslcourse
> > practicals for a bit more info:
> > http://www.fmrib.ox.ac.uk/fslcourse/seg_struc/_1110_fast_eg1.fpd/index.html
> > All the best,
> > Mark
> > Dr Krish Singh wrote:
> >> Hi,
> >> We have just started generating mp-rage volume scans from our new 3T Siemens
> >> Trio, using the 8-channel head coil.
> >> The images look great, with excellent grey-white matter contrast, but there
> >> is a noticeable bias field.
> >> Fast seems to make a great job of bias-correcting these images, but I have
> >> two questions:
> >> 1) I wonder whether it is possible (on the command line) to simply
> >> bias-correct the images, without doing the segmentation? Or does the
> >> segmentation not really contribute to the processing time?
> >> 2) Is it possible to apply the generated bias field image to another image
> >> (i.e. The non-skullstripped image)? Is it simply a matter of multiplying in
> >> avwmaths?
> >> Thanks and all the best,
> >> Krish
> >> --
> >> Dr K.D. Singh
> >> Senior Lecturer and Convenor of the Neuroimaging Research Group,
> >> Director, MRI Research Centre,
> >> Neurosciences Research Institute
> >> Aston University, Birmingham B4 7ET, U.K.
> >> Tel/Fax: +44 (0)121 [359 3611 ext 5176/5190]/[333 4220]
> >> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group,
> Director, MRI Research Centre,
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [359 3611 ext 5176/5190]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
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