External Email - Use Caution

Hello,

I produced an m3z warp file with mri_gradunwarp.

Now I need to 0 out all displacement in the z direction, while keeping everything else the same since I need to combine multiple warps from images with different geometries.

I see two strategies:

(1) working directly on the m3z file

I could not get mri_convert or mris_calc to do the trick. I thought I nailed it by manually editing the m3z file in freeview, but freeview saves the results in mgz format :-( Is there anything else I missed?

(2) converting to mgz or nii timeseries, manupulate those and convert back to m3z

mri_convert produced a nii file that freeview could not read and a single-frame mgz file that looks like some mishmash of the original 3-frame m3z.

Any idea on how I can acheive my goal?

A word on why would I want to do this silly thing. I have single-slice EPI and fov-matched higher-inplane-resolution single-slice GRE images. They have different within-slice gradient-non-linearity-related distortions. I want to undistort the GRE image then distort it to the EPI space. I need to zero out through-plane distortions to avoid displacing signal outside the imaging grid. Ignoring through-plane distortions should not be a problem for overlaying my GRE and EPI since, unlike within-plane distorsions, through-plane distortions are matched.

Thanks a lot for the help and

Have a very good day!

Sebastien

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer