Hello,
I have some analyze
images (128*128*68), and I did not
understand the way to read them correctly (with mri_convert).
For the moment I am using
: ‘mri_convert chuv70 –it
img –ot mgz 001.mgz’. This command works but gives me INFO:
could not find …mat file for direction cosine info.
In the end of my
processing I have to get my output (coming
from mri_label2vol command) according to a template that I have made
128*128*128
(empty_cube.img), then convert it to my orientation with a software
(imageconverter) then cut the additional slices to obtain the
FreeSurfer
output in the same referential as my original data to continue my
processing in
matlab (windows).
I also open one of dicom
(axial slice) file with matlab and
see the ImageOrientationPatient field: it is
-0.0173 0.9999
-0.0005 0.0302 0.0000 -0.9995
I also tried to convert
this with mri_convert : Mri_convert
chuv70 –it dicom –ot mgz 003.mgz
It works and gives me..
Spatial
information
first image
position 72.7981 -128.026 125.594
last image
position 72.7981 -128.026 125.594
image
orientation -0.0172556 0.999851
-0.000521332 0.0301985 1.35525e-19 -0.999544
-------------------------------------------------
TR=9.99,
TE=4.60, TI=0.00, flip angle=8.00
i_ras
= (0.0172556, -0.999851, -0.000521332)
j_ras
= (-0.0301985, -1.35525e-19, -0.999544)
k_ras
= (0.999395, 0.0172635, -0.030194)
writing
to 003.mgz...
but I don’t know how to
use these informations to get
my output in the correct orientation ?
Could some one help me!!
Thanks
Leila