or, since the correct values display if I load the same MNC file with Matlab, it could be a problem with mri_binarize?
2014/1/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > then is seems like the problem is with your mnc, not with anything we are > doing, right? > > On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: > > same thing >> >> >> 2014/1/22 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> and what if you run it on the mnc? >> On Wed, 22 Jan 2014, Caspar M. Schwiedrzik wrote: >> >> 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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