you could also use:
mri_convert with the -rl (reslice like) option to change the volume back to
the scanner template
On Fri, 14 Dec 2007, Nick Schmansky wrote:
On Fri, 2007-12-14 at 15:57 -0500, Mishkin Derakhshan wrote:
Thanks.
It didn't quite work as I'm guessing the step sizes in original.mnc
are negative, but I am able to reshape the minc file afterwards to get
it exactly the same.
From my (limited) understanding of mri_vol2vol, when you invoke it
with the --regheader is it taking the ras to voxel transform as listed
from mri_info aseg.mgz and then applying that to the image to get into
the original.mnc space?
yes, I believe this is the case.
thanks,
mishkin
On Dec 13, 2007 11:47 PM, Nick Schmansky <[EMAIL PROTECTED]> wrote:
Mishkin,
try this:
mri_vol2vol --mov aseg.mgz \
--targ original.mnc \
--o aseg-in-native.mnc \
--regheader \
--interp nearest
Nick
On Thu, 2007-12-13 at 22:05 -0500, Mishkin Derakhshan wrote:
Hi,
I am having troubles getting the right options with mri_convert.
I ran:
recon-all -autorecon1 -i original.mnc -s subj1
recon-all -subcortseg -s subj1
I now want to convert aseg.mgz into aseg.mnc but in the same space and
with the same orientation as my original.mnc file.
My original.mnc file has the following attributes:
double zspace ;
zspace:comments = "Z increases from patient inferior to superior" ;
zspace:step = -0.9765625 ;
zspace:start = 127.418768256005 ;
zspace:direction_cosines = -0.0275245718714001,
-0.000514697647100001, 0.999620994692302 ;
double yspace ;
yspace:comments = "Y increases from patient posterior to anterior" ;
yspace:step = -0.9765625 ;
yspace:start = 146.850463958339 ;
yspace:direction_cosines = -0.0186971433325, 0.999825193136882,
-2.319984599e-08 ;
double xspace ;
xspace:comments = "X increases from patient left to right" ;
xspace:step = 1.49999999999996 ;
xspace:start = -95.4780255890689 ;
xspace:direction_cosines = 0.999446254069973, 0.0186900576545041,
0.0275293837630133 ;
short image(zspace, yspace, xspace) ;
Any help would be much appreciated.
thanks,
mishkin
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