We wanted to change from manually segmentation to fully automated segmentation of MRI scans from the whole body. We like to measure the Volume of muscle mass (legs, arms, trunk) and fat mass (SAT, VAT) in adults and children. I found MIPAV as freeware, but is it really full automated and can segment whole body data? Does anyone now an easy tutorial for this software? Or is there another validated software?
Hi Corinna,
I often use brain segmentation modules to separate different constituents of muscle from fat etc. For example, if you use FSL's FAST module, it will separate bone, fat, and muscle based on their different MR intensities. The key is to try different contrasts i.e. T2, FLAIR, T1, PD, etc, to see which works best. Sometimes I combine the scans (using fslmaths), so you may have to play with the data a bit to get the best separation.
Regards,
Jerome
Dear Jerome,
thank you very much for your answer. I just have seen FSL as tool for the segmentation of GM,WM and Cf of the brain. How could I use it for the segmentation of bone, fat and muscle? Is FSL Fast an extra module, which I need to download beside FSL and is mathlab needed? Thanks for your help!
Regards,
Corinna
Hi Corinna,
FAST (fMRIB's Automated Segmentation Tool) is part of the FSL package, so no need to download an extra module. To use it, type in fsl and then select FAST, or just type in Fast. Instead of selecting a brain scan as the input, just select your body scan.
Only FSL is needed, not Matlab.
Regards,
Jerome
Thanks for the informations Jerome, I will try to work it out with FSL.
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