Stephen Wilson

Zero sform_code and srow_x, etc. in segmentation image

Thank you Philip, I will read your script and see if it works for my data, or at least provides pointers to the right parameters. Indeed I can't get a field map here--these are pre-existing clinical scans that I'm just using for research after the fact.

Thank you Nick, these responses were all very helpful. I will post again when I have tried some of this out.

Thanks, yes I started with defaults based on the provided scripts, but didn't get great results. Here are some of the changes I am considering specific to my coreg context: (1) the SyN stage from the script has: -c [50x0,1e-6,10] -f 2x1 -s 1x0vox'] I changed this to: -c [1000x750x500,1e-7,20] -f 1x1x1 -s 5x2x0mm My reasoning: (i) why 0 iterations at the second step? (ii) require more convergence (iii) don't want to shrink at all in the z plane where voxels are 5 mm, so better not to shrink at all?...

I am using ANTS to coregister clinical acute stroke DWI scans with other modalities obtained at the same time on the same patient, e.g. FLAIR. As expected, there is significant geometric distortion of the echo-planar DWI sequences. I'm hoping ANTS can correct this to some extent. I'm using the antsRegistration binary with a rigid body step (in case there is patient movement between sequences) followed by SyN to deal with the distortion. Results so far are not as good as I hoped for. Critically, the...