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/
>
>
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