I'll be brave and answer this one - since I've asked the same questions
myself in the past...
1) As I understand it, the bias field estimations and segmentation
procedure run iteratively together, so you can't have one without the
2) Yes, but you need to output a dilated version of the bias field
(-oba option) and then run avwmaths_32R (i.e. need to have floating
point data). You can revert back to more sensibly sized bit depths after
you've multiplied by the bias field
fast -l 100 -i 8 -oba 100 <betted_input_image>
avwmaths_32R <input_image> <betted_input_image>_abias <output_image>
Clare E. Mackay, Ph.D.
Prince of Wales International Research Centre (POWIC),
University Department of Psychiatry,
Warneford Hospital, Oxford. OX3 7JX. UK
tel: 01865 455910 fax: 01865 455922
OCMR: 01865 221866 / 72
[log in to unmask] www.psychiatry.ox.ac.uk/powic
>>> [log in to unmask] 01-06-2004 13:00:59 >>>
We have just started generating mp-rage volume scans from our new 3T
Trio, using the 8-channel head coil.
The images look great, with excellent grey-white matter contrast, but
is a noticeable bias field.
Fast seems to make a great job of bias-correcting these images, but I
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
(i.e. The non-skullstripped image)? Is it simply a matter of
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/