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. > >
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