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
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