Hi Bruce,
mri_diff does not return any differences. However, when I load the MNC file into Matlab using loadminc (http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc), I do retain all the values between 0 and 255. Also, I have something like an annotation file for the MNC file that lists values between 0 and 255.
The MNC is unsigned byte.
Caspar


2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
how do you know that the values were there before? Try running mri_diff on the .nii and the .mnc and see if it finds any differences

Bruce


On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

Hi Bruce,
I have tried the two following commands, and various flags on mri_convert:
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




2014/1/22 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
      Hi Caspar

      hmm, I don't know why that would be the case. Can you send the
      full command line and screen output?
      cheers
      Bruce
      On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:

            Hi!
            I am having some troubles converting MNC files to
            NII while preserving the
            exact values in the MNC file. I have tried to use
            mri_convert and mnc2nii,
            but in both cases, the values in the file output get
            changed. The help of
            mri_convert mentions that the output for MNC files
            may not work.
            Is there a workaround or a recommended procedure to
            convert MNC into NII?
            Thanks, Caspar








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