[MINC-users] dcm2mnc vs 3D DICOM

[Robert D. Vincent]

Hi Alex,

That is surprising. There is only one position indicated in the file, and
we are correctly reading it as 0, 0, 0 (it's a DICOM element 0020, 0032).
So as far as we are concerned we're assigning the correct start values.

It's possible that dcm2nii is "inventing" position values corresponding to
the centre of the grid - are they something like 150.6? (128/2)*2.353

    -bert


On Thu, Feb 11, 2016 at 3:02 PM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hi Bert,
>
> Cool - thanks much! The steps/zspace now look good :-)
>
> However I believe that the starts may still be wrong. When run through
> dcm2nii - nii2mnc, the volume ends up with start values that I suspect are
> 'real' (they roughly match the corresponding T1 that I have). With this new
> dcm2mnc, the start values are all 0.
>
> -- A
>
> On Thu, Feb 11, 2016 at 2:34 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Alex,
> >
> > I just pushed a fix to Github that should put correct Z axis spacing in
> > these sequences.
> >
> >     -bert
> >
> > On Thu, Feb 11, 2016 at 10:59 AM, Gabriel A. Devenyi <gdevenyi at gmail.com
> >
> > wrote:
> >
> > > Just a follwup, the "newer" dicom creator is dcm2niix, may be able to
> > find
> > > some useful info here https://github.com/neurolabusc/dcm2niix
> > >
> > > --
> > > Gabriel A. Devenyi B.Eng. Ph.D.
> > > Research Computing Associate
> > > Computational Brain Anatomy Laboratory
> > > Cerebral Imaging Center
> > > Douglas Mental Health University Institute
> > > McGill University
> > > t: 514.761.6131x4781
> > > e: gdevenyi at gmail.com
> > >
> > > On Thu, Feb 11, 2016 at 10:47 AM, Robert D. Vincent <
> > > robert.d.vincent at mcgill.ca> wrote:
> > >
> > > > Hi Alex,
> > > >
> > > > We've encountered so little 3D DICOM over the years I'm not surprised
> > it
> > > > isn't handled well.
> > > >
> > > > Thanks for the dataset. I will look into it and let you know.
> > > >
> > > >     -bert
> > > >
> > > >
> > > > On Thu, Feb 11, 2016 at 10:33 AM, Alex Zijdenbos <
> zijdenbos at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi all,
> > > > >
> > > > > I got some 3D DICOM SPECT data that dcm2mnc issues with - depending
> > on
> > > > what
> > > > > version of dcm2mnc I use, I get somewhat different results; but in
> > most
> > > > > cases I end up with irregular z-spacing and/or a flipped z-axis.
> The
> > > most
> > > > > recent version I tried was dcm2mnc version 2.01.03 from
> minc-toolkit
> > > > > version 1.0.08.
> > > > >
> > > > > If I run the same thing through dcm2nii followed by nii2mnc
> (ugh!), I
> > > > > actually get a volume that looks like I expected. There appears to
> be
> > > > > coordinate space information in the 3D DICOM that dcm2nii seems to
> be
> > > > able
> > > > > to interpret, but dcm2mnc does not.
> > > > >
> > > > > Thoughts/pointers/updated versions of dcm2mnc?
> > > > >
> > > > > Here is a sample DICOM set:
> > > > > ​
> > > > >  s1_0013006_3006.dcm.gz
> > > > > <
> > > > >
> > > >
> > >
> >
> https://drive.google.com/file/d/0B5fOtqpIs4sKVVlVVVF0VTZ5Sjg/view?usp=drive_web
> > > > > >
> > > > > ​
> > > > >
> > > > > Thanks,
> > > > >
> > > > > -- A
> > > > > _______________________________________________
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