Re: [Freesurfer] .mat/.hdr and orientation

I would have thought that that mri_convert cmd (with .img) would have worked. what went wrong?

Susie Heo wrote:

Hello, I am hoping that someone can help me to solve my orientation/angle acquisition problem:

1. I have an EPI oblique slice in Analyze format with incorrect orientation/angle acquisition information in the .hdr file (no .mat file)
2. I have a distorted image of the same slice in Analyze format with the correct orientation/angle information in the .hdr/.mat files
3. I would like to change the .hdr/(.mat?) file of 1) to conform to the orientation/angle specs of 2).

I have tried:

1. Replacing 1).hdr w/ 2).hdr--incorrect orientation; image off center; same as if kept 1).hdr
2. Replacing 1).hdr w/ 2).hdr and 2).mat--correct slice angle, image flipped -y and possibly -x?
3. mri_convert <input> <output> --iid -1 0 0 -ijd 0 1 0 -ikd 0 0 1 where <input> = 1).img, 2).hdr, 2).mat --lost slice angle, correct orientation

Any tips? What exactly do the .hdr and .mat files contain?

Susie

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