[MINC-users] Odd behaviour with recent versions of dcm2mnc/mincreshape

[Alex Zijdenbos]

Hi all,

Stumbled into something rather strange:

$ dcm2mnc DICOM/ADNI_126_S_0709_MR_IR-FSPGR-Repeat MINC_dcm2mnc_2.3.01
$ mincheader MINC_dcm2mnc_2.3.01/*/*mnc | grep spacing
xspace:spacing = "regular__" ;
yspace:spacing = "regular__" ;
zspace:spacing = "regular__" ;
$ mincreshape MINC_dcm2mnc_2.3.01/*/*mnc MINC_dcm2mnc_2.3.01/reshaped.mnc
$ mincheader MINC_dcm2mnc_2.3.01/reshaped.mnc | grep spacing
xspace:spacing = "yspace" ;
yspace:spacing = "yspace" ;
zspace:spacing = "yspace" ;

In other words, the <dim>:spacing attribute gets mangled by what *should*
be a no-op. This is using:
$ dcm2mnc -version
program: 2.3.01 built Dec 10 2020 01:01:35
libminc: 2.4.03
netcdf : 4.5.0 of Jun 26 2018 10:58:21 $
HDF5   : 1.8.20

If I do the exact same thing with this older version:
$ dcm2mnc -version
program: 2.0.07 built Mar 19 2014 16:54:51
libminc: 2.2.00
netcdf : 3.6.1 of Mar 19 2014 16:53:18 $
HDF5   : 1.8.9

All seems to work as expected (all :spacing attributes remain "regular__").
Doing a quick comparison of the headers of the MINC volumes generated by
these two versions of dcm2mnc, a few differences appear:
$ diff <( mincheader MINC_dcm2mnc_2.0.07/*/*.mnc | grep spac | sort) <(
mincheader MINC_dcm2mnc_2.3.01/*/*.mnc | grep spac | sort)
3c3
< double xspace(xspace) ;
---
> double xspace ;
10d9
<  xspace = -100.899, -99.6994, -98.4994, -97.2994, -96.0994, -94.8994,
11a11
>  xspace = 97.1005 ;
14d13
< xspace:dimorder = "xspace" ;

Further, if I use the "new" mincreshape on the "old" volume or vice versa,
the spacing attributes remain "regular__". It's only the combination of
both "new" dcm2mnc and "new" mincreshape that results in this.

Unfortunately I can't actually distribute the source data, but it is ADNI
data, and this is not an isolated case - this pretty much happens on most
volumes that I pick up.

Anybody any idea what we might be looking at here?

Thanks,

-- A