[MINC-users] mnc2nii and mnc2ana

[Søren Christensen]

Hi,
 I am having trouble using mnc2nii and mnc2ana.
I run:
 mnc2nii se1.mnc se.nii
 nii2mnc se.nii se1n.mnc

and mincinfo gives:

file: se1.mnc
image: signed__ short 0 to 1462
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     19            7        -47.3
    yspace                    256    -0.859375       101.87
    xspace                    256    -0.859375       109.57


file: se1n.mnc
image: signed__ float 0 to 1026
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                     19            7        -66.5
    yspace                    256     0.859375         -110
    xspace                    256     0.859375         -110


I was wondering if someone has an explanation. The version is:

mnc2nii -version
program: 1.4
libminc: 1.4
netcdf : 3.6.0-p1 of Jun 10 2005 16:14:06 $



When doing the same back and forth procedure with mnc2ana descrepancies in step and start also arises. Spatially, mnc2nii -> nii2mnc throws the scan a bit off position while mnc2ana -> ana2mnc flips the x-axis and also change the start points numerically.



If anyone has a good way of using FSL's BET with MINC i'd be interested to hear about it!





Best regards
Soren