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