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

Tue Sep 5 17:56:52 EDT 2006

Hello Sylvain,

I get the following results <based on the scenario described earlier> :

] mincinfo -image_info InputFile.mnc
file: InputFile.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     50            3     -74.4609
    yspace                    256    -0.859375      108.378
    xspace                    256     -0.85938          115

] mincinfo -image_info OutputFile.mnc
file: OutputFile.mnc
image: signed__ float 0 to 1285.8984375
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     50            3     -74.4609
    yspace                    256     0.859375     -110.762
    xspace                    256      0.85938     -104.142

Should I be worried about a change from 'singed short' to 'signed float'?

Cheers,
Thor

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

-- 

Thorarin Bjarnason, BEng, MASc
www.imaginginformatics.ca