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
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