[MINC-users] dcm2mnc vs 3D DICOM

[Alex Zijdenbos]

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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