Hi everyone,
following some success by a colleague of mine in getting fsl-vbm to
work on rat brain data, I am following the tutorial at:
http://www.fmrib.ox.ac.uk/fsl/fslvbm/index.html
As my colleague found out, rodent brain extraction is not similar
enough to human brain extraction to reliably use fsl's BET. For the
record, the Brainstrip plugin to MIPAV[1] requires minimal manual
tweaking of the mask after running the algorithm and is fairly
feasible, so long as your sample sizes don't run into the hundreds.
My question: I now have the extracted brain datasets (.nii format;
orientation as required by fslvbm), and would like to see how good a
job fslvbm_2_template would do on these data. Is there a way of
running fslvbm_1_bet so it does all the file conversions _without_
performing any extraction, so that I can put my extracted data in a
format that fslvbm_2_template can work on? I think tbs_1_preproc used
to be able to do this, but it is no longer used in the updated fslvbm.
Also, as I supect that a 2mm cube is not really good enough resolution
to perform accurate registration on a rat brain, I have simply 'blown
up' my datasets by multiplying the voxel sizes of my rat brains by 10
in the image header. Does anyone see a problem with doing this?
Many thanks for your help,
Chris
[1] See: Bazin et al (2007), J Neurosci Meth 165:1, 111-121.
--
Christoph Blau, MVB
Trinity College Institute of Neuroscience
Lloyd Building
Trinity College
Dublin 2
Ireland
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