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

[Thorarin Bjarnason]

Hello:

Thank you for your help.

I guess I did not tell the whole story <by accident, of course>.

The problem might originate from converting dcm2mnc. When I ran this
command to convert the dicom volume I had a warning:

> dcm2mnc * .
Checking file types...
File Img000.dcm appears to be DICOM (CD/Export).
Parsing 50 files     |<--------------------------------------------------->|
Sorting 50 files...   Done sorting files.
Processing files, one series at a time...
-Parsing series info |<--------------------------------------------------->|
WARNING: calculated slice width (2.9271522383) disagrees with file's
slice width (3.0000000000)
-Creating minc file  |<--------------------------------------------------->|
Done processing files.

So perhaps this warning caused an error later on. I have a work around though:

] dcm2mnc * .
] mnc2nii InputFile.mnc Temp1.nii
] nii2mnc Temp1.nii Temp2.mnc
] nu_correct -options Temp2.mnc OutputFile.mnc

nu_correct ran to completion this time. Can anyone comment as to
whether this workflow is OK?

Have a nice day,
Thor

On 9/5/06, Sylvain MILOT <sylvain at bic.mni.mcgill.ca> wrote:
>
>
> 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
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


-- 

Thorarin Bjarnason, BEng, MASc
www.imaginginformatics.ca