[MINC-users] Problem with nu_estimate_np_and_em

[Andrew Janke]

On 5/10/05, haytham@umich.edu <haytham@umich.edu> wrote:
> when I run the following command
> 
> nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.01
> -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute
> -clobber -nokeeptmp manconv_02_t1_final_tmp.mnc /manconv_02_t1_final.imp
> 
> I get this message:
> 
> Transforming slices:..............................................Done
> Error: Composite mask volume is empty.  Check for one of the following:
>  1) the user supplied mask is empty (all zeros)
>  2) the values within the region of interest are entirely less than one
>  3) the user supplied background threshold is too high
>  4) the intersection of the various masking options yields an empty mask

I have seen this when the generated (automatic in your case --
-automask) mask is indeed all 0 only.  Perhaps remove the nokeeptmp
and have a look at the intermediate mask file.  You may have to
provide a manually selected mask threshold.


-- 
Andrew Janke      (a.janke@gmail.com || www.cmr.uq.edu.au/~rotor)
Australia->Brisbane     H: +61 7 3390 6332  || M: +61 4 2138 8581