[MINC-users] dcm2mnc vs 3D DICOM

[Alex Zijdenbos]

Hi Bert,

Yes - converting to nii and then to MINC yields this volume:

image: signed__ short 0 to 32766
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     65        3.138     -101.985
    yspace                    128        2.353     -150.592
    xspace                    128        2.353     -150.592

So I suspect you are right... Either way is fine with me in practice, I
just wanted to make sure the conversion wasn't dropping information.

Thanks!

-- A


On Thu, Feb 11, 2016 at 3:43 PM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> 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
> > > > > > _______________________________________________
> > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > >
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> > > > >
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