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