mnc2nii -nii -int paxinos-MNI.mnc paxinos-MNI.nii
mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
Yhe output of the latter would be:
mri_convert -i paxinos-MNI.mnc -o paxinos-MNI.nii
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from paxinos-MNI.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to paxinos-MNI.nii...
for mri_convert, --nochange, -odt float/int/uchar, --no_scale 1 all do not make a difference.
It could be that the problem arises once I call mri_binarize afterwards. I know that there are values between 1 and 256 in the MNC file, but when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files, it does not find any values lower than 53 or so.
Caspar