I've found that BET does not easily work with non-human sizes, and have worked around it by redefining the pixdim fields (with different factors in x,y vs z) so that the rat brain appears to have human size and shape to the program. fsl has easy tools for redefining header fields without having to change actual data.
Mike Rohan
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Rats [[log in to unmask]]
Sent: Monday, December 12, 2011 7:25 PM
To: [log in to unmask]
Subject: [FSL] Rodent / Rat TBSS Registration
Hi All,
I have DTI data from rodent / rat brains that I would like to process through TBSS. Since this is non-human data, I anticipate that I will need to make some changes to the scripts, but I am unsure what those changes need to be. I do plan on using the -n flag at the tbss_2 stage to determine the most representative target. After that I'm at a loss. I know that it registers to the MNI152 brain at some point (tbss_3), and I suppose I don't want that to happen. Could anyone tell me the specific changes I would need to make in the scripts to enable us to complete the process on rodent data (running FSL 4.1.8)?
Thank you for your help.
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