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You might be able to convert it to a nifti (eg, with mri_warp_convert
--outfsl), do your optionations, then convert it back to m3z
On 6/14/2023 4:08 PM, Proulx, Jean Sebastien wrote:
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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
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