Re: [Freesurfer] analyze orientation

It is just looking for a .mat file (commonly found with SPM analyses). The bottom line is that everything is ok if it is oriented properly in tkmedit. Be careful, though, as you may or may not be able to tell whether it is LR reversed.

Leila BH wrote:

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

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