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

[Andrew Janke]

> 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>


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