Jun, the "--out_orientation" is probably not what you want. As the documentation says,

NOTE: THIS IS ONLY TO BE USED WHEN THE ORIENTATION INFORMATION IN THE INPUT FILE IS *WRONG*. IF IT IS CORRECT, THIS WILL MAKE IT WRONG!

if you're starting with dicom, it is very probably right. Is there a reason you think it would be wrong. What are you trying to do?

doug

Xu, Jun wrote:

Hi,

I was trying to create affine matrix from DICOM file and compared with the one created by mri_convert.

For T1 image, if I use mri_convert

...

mri_convert –it dicom [in filename] –ot nii [out filename]

The affine matrix (srow*) part get from load_nii_hdr.m command is

Affine I:

srow_x: [0 0 -1.2000 92.2031]

srow_y: [-1 0 0 132.7965]

srow_z: [0 -1 0 131.8291]

which is the same affine matrix I got directly from DICOM file according to the description in nifti header doc.

*However,* if I use

...

mri_convert –it dicom [in filename] –ot nii [out filename]

–out_orientation PRS

The affine matrix (srow*) part get from load_nii_hdr.m command is

Affine II:

srow_x: [1 0 0 -123.7969]

srow_y: [0 -1 0 140.7965]

srow_z: [0 0 1.2000 -92.1709]

That I do not know how to create. I know the orientation is changed from PSR (T1 sag original) to RPS (specified in out_orientation). Could you tell me what I can do in order to obtain

an affine matrix II from affine I?

Thanks.

Jun

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