Dear FSL users/experts,
Hi. I sent this message a few days ago, with no responses. Hope I can get some advice on this, thanks!
I have seen a number of posts related to this, as well as the fnirt webpage, but just wanted to make sure I am doing this correctly.
I have high-resolution structural data (T1), EPI data and field maps, and would like to register the structural image (and associated atlas) to my DTI images, correcting for EPI distortion in the process.
1) Using epi_reg to register the structural image to the EPI image, specifying the fieldmap to distortion-correct the EPI
2) Convert the warp field output (.mat file) to nii.gz format using convertwarp, without the field shift, this will give us the warp field from undistorted EPI space to T1 space.
3) Use fugue to undistort my DTI images, with the "shift field" output from epi_reg
4) Use invwarp to invert the output warp field from epi_reg - this gives us a warp field from T1 to undistorted DTI space.
5) Use applywarp with this inverted warp field to warp the atlas to the undistorted DTI image.
Here are the commands used:
1) epi_reg --epi=magDTI.nii.gz --t1=T1W_3D_TFE.nii.gz --t1brain=T1WBrain.nii.gz --out=DTI_to_T1W.nii.gz --fmap=B0map_fieldmap_rads.nii.gz --fmapmag=B0map_mag.nii.gz --fmapmagbrain=B0map_magBrain.nii.gz --wmseg=T1W_fast_wmseg.nii.gz --echospacing=.0004119414299242 --pedir=y --noclean
where magDTI is a mean b0 image
2) convertwarp -r T1WBrain.nii.gz --postmat=DTI_to_T1W.mat -o DTI_to_T1W_warp2.nii.gz
3) fugue -i DTIimage --loadshift=DTI_to_T1W_fieldmaprads2epi_shift.nii.gz -u DTIimage_Unwarped.nii.gz
4) invwarp -w DTI_to_T1W_warp2.nii.gz -r DTI_Unwarped.nii.gz -o T1W_to_DTI_warp.nii.gz
5) applywarp -i T1_Atlas.nii.gz -r DTI_Unwarped.nii.gz -w T1W_to_DTI_warp.nii.gz -o T1_Atlas_to_DTI.nii.gz --interp=spline --rel
If I understand this correctly, this will give me the structural T1 atlas image in undistorted EPI space.
Any advice/suggestions for this approach would be greatly appreciated.
Best,
Mark Wagshul
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