Hi,
If you have the T2 and T1 aligned, and generate a brain mask from the
T2 image, you can easily apply this to the T1 just using fslmaths:
fslmaths T1 -mas T2-brain-mask T1_brain
Cheers.
On 11 Oct 2007, at 00:04, William Janes wrote:
> All,
>
> I am attempting multi-channel segmentation of brains with a variety
> of stroke lesions. While segmentation with mfast seems painless,
> the initial BET brain extraction is problematic.
>
> BET does quite well at extracting our T2-weighted images at it's
> default settings. The T1-weighted images, however, do not extract
> cleanly. I have tried numerous iterations, adjusting the fractional
> intensity threshold, using -R, -S, or -A2, and all result in
> erroneously included and excluded voxels. That is, an unacceptable
> amount of grey matter is removed and a great deal of bone, muscle,
> and other tissue remains. In addition, large swaths of more shallow
> lesions are excluded, defeating the purpose of the process.
>
> The T1 and T2 images have already been transformed to the same
> atlas space. Given that, along with the quality of our T2 BET
> extraction, does the following solution sound reasonable?
>
> - Use 'bet -m' to extract the T2 and generate a binary mask
> - Use the mri_mask tool from Freesurfer to apply the T2 mask to the
> T1 image
> - Proceed with mfast using the extracted T2 and the masked T1
>
> Alternatively, if this process sounds inappropriate, does anyone
> have suggestions for better T1 extraction?
>
> Thank you for any help you can provide.
>
>
> William E. Janes
> OTD Student
> Washington University School of Medicine
> Program in Occupational Therapy
> Campus Box 8505
> 4444 Forest Park Avenue
> St. Louis, MO 63108
> (618) 973-5344
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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