[MINC-users] N3 crashes when processing a volume on MacOSx

[Sylvain MILOT]

Hello,

I haven't used nu_correct in a long while but one thing caught my eye:

Files /var/tmp/nu_correct_7953//test_field.mnc and InputFile.mnc have
> different step coordinates (zspace)
> nu_evaluate: crashed while running mincmath (termination status=256)

mincmath requires that all its input data have the same shape and
same coordinate sampling.

try nu_correct -keeptmp ... to troubleshoot.

hoe this helps,

Sylvain

On Tue, 5 Sep 2006, Thorarin Bjarnason wrote:

> Hello All,
>
> I recently got minc tools running on Mac OS X 10.4.7 < with effort ;-)
> >. I am interested in running N3. I have no trouble taking one file
> from a dicom set and processing it <by converting it to mnc and
> running nu_correct>. Processing an entire volume is not working as
> well, unfortunately. Everything appears to be running fine until the
> end <I think> where nu_correct crashes. My work flow is as follows:
>
> I convert dicom to mnc using:
> dcm2mnc * .
>
> I go to the mnc output dir and use the following command:
> nu_correct -fwhm 0.15 -distance 50 -stop 0.0001 -iterations 1000
> InputFile.mnc test.mnc
>
> and the computer works away for a while with the following output:
> Processing:..............Done
> Not implemented yet in cache_volume_range_has_changed()
> Not implemented yet in cache_volume_range_has_changed()
> Processing:..............Done
>       ... etc ...
> Not implemented yet in cache_volume_range_has_changed()
> Not implemented yet in cache_volume_range_has_changed()
> Number of iterations: 138
> CV of field change: 9.77015e-05
> Transforming slices:..................................................Done
> Not implemented yet in cache_volume_range_has_changed()
> Not implemented yet in cache_volume_range_has_changed()
> Transforming slices:..................................................Done
> Files /var/tmp/nu_correct_7953//test_field.mnc and InputFile.mnc have
> different step coordinates (zspace)
> nu_evaluate: crashed while running mincmath (termination status=256)
> nu_correct: crashed while running nu_evaluate (termination status=256)
>
> A test.imp file was created. I tried changing some of the imput
> parameters when I call the nu_correct function, but I get the same
> error.
>
> Does anyone know how I can fix this error?
>
> Kind Regards,
>
> --
>
> Thorarin Bjarnason, BEng, MASc
> www.imaginginformatics.ca
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

---
Sylvain Milot (sylvain at bic.mni.mcgill.ca)
              (trinity at bic.mni.mcgill.ca)
Brain Imaging Centre
Montreal Neurological Institute
Webster 2B, Room 208
Montreal, Qc., Canada, H3A 2B4
Phone  : (514) 398-4965, Fax: 398-8948
Mobile : (514) 712-1768
Office : 527 Av Des Pins O., Room 204
         Montreal, Qc., H2W 1S4