Hi Bruce,
I am confused, too.
If the conversion is proper, why does mri_binarize not find values below ~53? when I call mri_binarize with -match on the MNC file or on any of the converted NIFTI files?
Caspar




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

now, I'm confused. So it sounds like mri_convert is doing the conversion properly then?

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

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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