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 <fis...@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 > > > > > > > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
