Can you describe the potential problem with mri_binarize more fully?
> <mailto:fischl@nmr.mgh.harvard.edu>>
On 01/22/2014 12:50 PM, Caspar M. Schwiedrzik wrote:
> 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 <fischl@nmr.mgh.harvard.edu
>> <mailto:fischl@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 <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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 <fischl@nmr.mgh.harvard.edu
> can you send us the full command line and> <mailto:fischl@nmr.mgh.harvard.edu>>
> 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
> <mailto: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
> <fischl@nmr.mgh.harvard.edu <mailto: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
>
> _______________________________________________> 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
>
>
>
>
>
>
>
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