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

[Sylvain MILOT]

Hello,

seems like an overkill - I would guess that dcm2mnc fails to set some
step/start values and that mnc2nii/nii2mnc uses some defaults values which
may not be correct - but for nu_correct's sake, I dont think it matters.

What does mincinfo reveal on both volumes?

 On Tue, 5 Sep 2006, Thorarin Bjarnason wrote:

> 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
> _______________________________________________
> 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