Greetings all. I'm trying to eliminate major inhomogeneity from a run of
70 T1 structural (Allegra 3T head coil) on which we will be doing
regional gm/wm/csf analysis.
To that end I'm multiplying (avwmaths_32R -mult) the original volumes by
their individual "fast -oba" output to try to eliminate the bias field
(a la http://www.aston.ac.uk/lhs/research/facilities/mri/biascrt.jsp).
My question: is there documentation describing the practical ranges of
fast's -l, -i, and -oba options for this purpose? If not I'd welcome
input on the effective range of each option. I'm shooting for decent
inhomogeneity correction and *reasonable* CPU time (an hour per brain
would be nice).
My approach thus far: The field inhomogeneity originally manifest itself
on the un-bias-field-corrected CSF volumes (_pve_0), which show a high
probability of CSF in places they shouldn't (e.g. dorsal third of
frontal lobes). To remedy I've been trying different combinations of
fast's -l -i and -oba values and then using avwstats -V to compare the
number of non-zero voxels in the resultant segmented CSF volumes.
Example: fast -n -l 100 -i 8 -oba 100 produces far more CSF voxels than
fast -n -l 125 -i 16 -oba 100.
I've also noticed that we experience many minutes with little processor
utilization before the first Main Iteration starts (and maybe even
before each subsequent iteration). Any idea why we're not getting full
CPU usage during this period? Trying to cut down on the current 30+
hrs/brain (Pentium IV's 2.8+).
Any help greatly appreciated!
--
Stephen Towler
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352-294-0048 office
352-258-6409 mobile
352-392-8347 fax
Leonard Lab
Department of Neuroscience
PO Box 100244
University of Florida HSC
Gainesville, FL 32610
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