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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)
completely.

I've written some instructions (including an automating script) at the
following webpage:

http://www.aston.ac.uk/lhs/research/nri/mri/Methods/BiasCorrect/

Might be be useful for some people.

Thanks again for another great tool!

Krish


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/