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 <fis...@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 <fis...@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 <fis...@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 >> <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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