[MINC-users] N3

[Jason Lerch]

Make sure that the intensity histogram of your volumes is adequate for 
N3 - which means that it should not lie between 0 and 1. If the actual 
values don't matter to you, try multiplying the volume with a large 
enough constant, then run N3.

Hope this helps,

Jason

joel-bruss at uiowa.edu wrote:

>Currently I have data from a GE 1.5T, and Siemens 1.5 and 3T (Avanto and Trio)
>scanners.  I am looking for a way to bias-correct these images so that they can
>be used with Gray/White segmentation and other volumetrics.  My data is in
>16-bit Analyze format and I have a minc converter (ana2mnc).  When I run
>nu_correct, with default parameters (-V1.0) as well as specifying a mask of the
>brain image, I get very awful results.  In my 124-slice volume, there are
>regions where the image is totally washed out (5-10 slice runs) and others where
>the brain looks nice but the bias-correction happened outside of the skull. 
>When specifying for temp files to be saved as well as a tempdir, after
>converting the bias field, it looks like a perfectly uniform smoothing kernel
>(ovular/egg shape) which is definitely not what the bias appears as (more polar,
>specifically in the frontal lobe).  I've tried downloading the test data but am
>unsure of how to even work with it.  I've read Sled et al's IEEE paper but don't
>find it that useful in configuring nu_correct.  Also, I set the max iteration
>for 150 but it runs through 3 iterations (in about 2 minutes) and says that it
>is done.  Is this really possible?
>
>Is there a help file, other than the README, or tutorial out there?  Any
>suggestions on how to configure nu_correct?  Should I use a different Minc
>converter?  Is it OK to use 16-bit images or do they need to be 8-bit?  Any help
>would be useful right now.
>
>Thanks for your time
>
>-Joel
>
>
>
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