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
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:
> All the best,
> Dr Krish Singh wrote:
>> 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
>> Thanks and all the best,
>> 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/