[MINC-development] nu_correct on linux

[Richard Boyes]

dear peter,

thanks for your feedback - unfortunately it crops up with a different
error, this time:

rboyes@gyrus:~/cvs/bias-correct-regress/custom-sw/regress/data/junk
rawtominc -byte -obyte -clobber -input ./bmask00000.img -coronal -xstep
0.9766 -ystep 1.8000 -zstep 0.9766 -range 0 255 -real_range 0 255
./bmask00000.mnc 120 256 256
rboyes@gyrus:~/cvs/bias-correct-regress/custom-sw/regress/data/junk
nu_correct -clobber -mask ./bmask00000.mnc ./00000.mnc
/correct00000.mnc  -stop 0.0005 -fwhm 0.075 -distance 100 -iterations
350 -mapping_dir . -shrink 3
Transforming slices:.........................................Done
No points were chosen by the specified criteria
resample_labels: crashed while running extracttag (termination status=256)
nu_estimate_np_and_em: crashed while running resample_labels (termination
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=256)

i've tried running nu_correct without the mask (below), but i'm getting the
problem of 1e-27 field change again. any other ideas, or can i send
you any other information?

rboyes@gyrus:~/cvs/bias-correct-regress/custom-sw/regress/data/junk
nu_correct -clobber ./00000.mnc ./correct00000.mnc -stop 0.0005 -fwhm
0.075 -distance 100 -iterations 350 -mapping_dir . -shrink 3
Processing:.........................................Done
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Number of iterations: 1
CV of field change: 7.88338e-27
Transforming slices:.........................................Done
256+0 records in
256+0 records out
Not implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_changed()
Transforming
slices:.....................................................................
...................................................Done


thanks, richard.


> -----Original Message-----
> From: minc-development-admin@bic.mni.mcgill.ca
> [mailto:minc-development-admin@bic.mni.mcgill.ca]On Behalf Of Peter
> NEELIN
> Sent: 05 January 2004 03:02
> To: Richard Boyes
> Cc: MINC
> Subject: Re: [MINC-development] nu_correct on linux
>
>
> On Tue, 23 Dec 2003, Richard Boyes wrote:
>
> > when i try nu_correct, it jumps out straight away,
> > saying the field change is 1E-27. this has happened
> > for multiple images with bad bias fields, which doesn't
> > seem correct.
>
> If I recall correctly, nu_correct had some difficulties with masks that
> had ranges that did not correspond to its expectations (is that correct,
> John?). This is just a guess, but try using the -scan_range option for the
> mask images as well:
>
> #Mask file - no need to swap bytes
> rawtominc -byte -obyte -clobber -input ./bmask00000.img -coronal \
>    -xstep 0.9766 -ystep 1.8000 -zstep 0.9766 \
>    -orange 0 255 -scan_range ./bmask00000.mnc 120 256 256
>
> Alternatively, replace the -orange option with
> "-range 0 255 -real_range 0 255" and do not use -scan_range.
>
>             Peter
> ----
>             Peter Neelin (neelin@bic.mni.mcgill.ca)
>
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