mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rdata3/space3/data/cschwiedrz/cooked/anatomicals/mni_macaque cmdline mri_binarize --i paxinos-MNI.nii --match 1 --o labels/1.nii sysname Linux hostname wiener machine x86_64 user cschwiedrz
input paxinos-MNI.nii frame 0 nErode3d 0 nErode2d 0 output labels/1.nii Binarizing based on matching values nMatch 1 0 1 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done
2014/1/22 Bruce Fischl fischl@nmr.mgh.harvard.edu
can you send us the full command line and screen output of the mri_binarize command?
On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote:
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 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.