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Oct 1, 2017 08:10 PM | Gina Joue
susceptibility distortion correction for T2*w
Hi,
I would like to use CMTK to correct susceptibility distortion in our T2*-weighted EPIs and am having problems where the corrected images look like the images were overlapped with a mirrored version (see attached) -- which perhaps is already apparent in the distortion/Jacobian determinant map. I was trying to roughly follow "Unwarping Echo Planar Images Using CMTK" as a guide although we are not dealing with diffusion-weighted images.
For some sessions, we only have an additional gradient echo image in the reverse phase-encoding direction as our T2*-weighted images. In this case, I treated a random T2*-weighted EPI image as b0_fwd and the extra GRE blip reverse image as b0_rev, which I fed as inputs to epiunwarp. I then applied the resulting Jacobian determinant from epiunwarp to all the T2*-weighted EPIs (as inputs to reformatx and imagemath).
For other sessions, we also have acquired two spin echo images with the same parameters as our T2-weighted EPIs in different phase encoding directions to each other. I treated these SE images as the b0_fwd and b0_rev inputs to epiunwarp.
Either way, we are having the same problem, and I want to say with my naive eye that this is already a problem during epiunwarp (hence I'm not including all the code here yet to reduce visual clutter). Could someone point out what I am doing wrong? I've tried the --no-flip switch, our images are acquired A-P (so I didn't change the default --phase-encode switch).
Could someone also explain to me why it is necessary to run and imagemath (step 3 "pixel-weise computations, outputting the distortion-corrected image" in the pdf guide to unwarp EPIs) after running reformatx which "applies the computed deformation to correct for susceptibility" (what is this set up applying and outputting if imagemath seems to be doing the applying and outputting)?
Many thanks in advance for any help and advice!
g
I would like to use CMTK to correct susceptibility distortion in our T2*-weighted EPIs and am having problems where the corrected images look like the images were overlapped with a mirrored version (see attached) -- which perhaps is already apparent in the distortion/Jacobian determinant map. I was trying to roughly follow "Unwarping Echo Planar Images Using CMTK" as a guide although we are not dealing with diffusion-weighted images.
For some sessions, we only have an additional gradient echo image in the reverse phase-encoding direction as our T2*-weighted images. In this case, I treated a random T2*-weighted EPI image as b0_fwd and the extra GRE blip reverse image as b0_rev, which I fed as inputs to epiunwarp. I then applied the resulting Jacobian determinant from epiunwarp to all the T2*-weighted EPIs (as inputs to reformatx and imagemath).
For other sessions, we also have acquired two spin echo images with the same parameters as our T2-weighted EPIs in different phase encoding directions to each other. I treated these SE images as the b0_fwd and b0_rev inputs to epiunwarp.
Either way, we are having the same problem, and I want to say with my naive eye that this is already a problem during epiunwarp (hence I'm not including all the code here yet to reduce visual clutter). Could someone point out what I am doing wrong? I've tried the --no-flip switch, our images are acquired A-P (so I didn't change the default --phase-encode switch).
Could someone also explain to me why it is necessary to run and imagemath (step 3 "pixel-weise computations, outputting the distortion-corrected image" in the pdf guide to unwarp EPIs) after running reformatx which "applies the computed deformation to correct for susceptibility" (what is this set up applying and outputting if imagemath seems to be doing the applying and outputting)?
Many thanks in advance for any help and advice!
g
Threaded View
Title | Author | Date |
---|---|---|
Gina Joue | Oct 1, 2017 | |
Torsten Rohlfing | Oct 3, 2017 | |
Gina Joue | Oct 4, 2017 | |
Torsten Rohlfing | Oct 5, 2017 | |