[MINC-users] dcm2mnc vs 3D DICOM

[Robert D. Vincent]

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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