[MINC-users] dcm2mnc and (ir)regular spacing?

[Alex Zijdenbos]

On Sun, Jan 8, 2012 at 6:16 PM, Andrew Janke <a.janke at gmail.com (mailto:a.janke at gmail.com)> wrote:
> > WARNING: Coordinate spacing (4) differs from DICOM slice spacing (5)
> >  (perhaps you should consider the -usecoordinates option)
> >  Using 5 for the slice spacing value.
> > 
> 
> 
> I did note the "irregular" in the zspace in the header you sent.
> 
> > Without -usecoordinates, the resulting volume has a zstep of 5mm and
> > is visually correct (in register); however, it still has the same list
> > of zspace coordinates that are 4mm apart. Besides the fact that that
> > is internally inconsistent, whenever I resample the volume it
> > immediately comes out 'squashed' again, so I assume that mincresample
> > relies on the explicit list of coordinates.
> > 
> > So it seems that dcm2mnc cannot handle these DICOM data properly
> > somehow (or the DICOM itself is bad).
> > 
> 
> 
> In 100% of the cases I have seen with this it is DICOM that is
> inconsistent. By this I mean that the various manufacturers treat
> these fields differently. Some include the slice gap in the slice
> width, some don't. Thus the option.
> 
> > Is there a way to remove the list of zspace coordinates from the MINC
> > header (other than by turning the volume into a stack of slices and
> > re-assembling it again)?
> > 
> 
> 
> This is my method:
> 
>   minc_modify_header -sinsert zspace:spacing="regular_" <file.mnc>

Well that sets the zspace:spacing attribute; but if the header still contains an explicit list of coordinates, then those wil be used by things like mincresample. Here is the whole MINC volume:

test.mnc (http://cl.ly/2h1h1O1i3G0H0S1i0w1k)

Try to resample this like like so:

mincresample -zstep 5 test.mnc test_z5.mnc

and then pull both volumes up in register :)

-- A