I would strongly suggest that you not use analyze format for exactly this reason. Tru using nifti and see if the problem persists.

doug

XJ Kang wrote:

Hi,

I am confused by the L/R of the images from mri_convert. Below are what I have:

anat.img: anatomical image from scanner, with brain left-side marker appeared on the image left in SPM.

I did the following steps: % mri_convert anat.img 001.mgz 001.mgz: brain left-side marker appeared on the image right in tkmedit, flipped L/R compared to anat.img % rmi_convert 001.mgz anatFS.img anatFS.img: brain left-side marker appeared on the image right in SPM, same as 001.mgz, not as the original anat.img

This means I cannot get to the original image orientation by mri_converting twice.

I also tried the following: %mri_convert 001.mgz --out_orientation RAS anatR.img %mri_convert 001.mgz --out_orientation LAS anatL.img

anatR.img and anatL.img appeared the same orientation in SPM, although they have different Analyze matrices.

My question, anyway I can flip the left/right of the mgz images using mri_convert?

Thank you for clearing this.

XJ Kang _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer