[MINC-users] using N3 - parameter values

[Jason Lerch]

On 20-Sep-06, at 5:20 PM, Thorarin Bjarnason wrote:

> Hello All,
>
> How does one use N3? What flags do users generally set? When I run the
> default, there are very little changes. Randomly setting flags seems
> hardly scientific  :-).

The default should work on 1.5T images. The most important parameters  
for nu_correct to play with are:

-mask binary_mask.mnc -> limits the processing to a region of  
interest - usually a good idea.
-distance -> lowering the distance to less than the default of 200 is  
often a good way of removing stronger inhomogeneities.
-fwhm -> lowering the width of the deconvolution kernel can also  
increase accuracy.

Another good tool to know is imp2field. nu_correct outputs two files  
- the corrected minc file and the field that it found (and removed).  
To actually view the field you have to turn it into a minc file first  
- this is what imp2field does.

Hope this helps,

Jason

>
> I realize these questions are simple, but I'm having trouble finding
> solutions on the web. Can anyone profide advice or point me towards
> some documentation?
>
> Cheers,
>
> -- 
>
> Thorarin Bjarnason, BEng, MASc
> www.imaginginformatics.ca
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> MINC-users at bic.mni.mcgill.ca
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