unwarping epis using fieldmaps - github...
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Unwarping EPIs using fieldmaps
Alex Huth MRI analysis clinic
March 16, 2015
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What is warping?• PE-axis distortion due to B0 inhomogeneity
A-P P-A
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What affects warping?
• Echo spacing
• Longer echo spacing is bad
• GRAPPA reduces effective echo spacing by GRAPPA factor
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Warping can be corrected (ish)
• Using a fieldmap
• A fieldmap shows how the B0 (main magnetic field) changes across your sample
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How do I get a fieldmap?
• gre_field_mapping sequence
• Acquires 2 GRE images with slightly different TE’s (e.g. 5.5ms and 7ms)
• Outputs magnitude and phase difference images
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How do I get a fieldmap?Magnitude image Phase difference image
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Fieldmap preprocessing• IMPORTANT: masking the magnitude image
• The mask should be TOO TIGHT, never TOO LOOSE
$ bet mag.nii masked.nii -‐R -‐m -‐f 0.5 -‐g 0.0
Vertical GradientThreshold
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Fieldmap preprocessing• Latest FSL has great tool for fieldmap processing
$ fsl_prepare_fieldmap SIEMENS phasediff.nii masked.nii field_map.nii 2.46
Delta TE (ms) from fieldmap
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Mask erosion is greatUsing mask from BET Using eroded mask
BAD
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Fieldmap regularization
• FSL’s FUGUE has great tools for fixing bad field maps
• Lots of available methods (see FUGUE docs)
• Despike and median filter seem to work the best (for me)
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Unwarping• Unwarp using FSL’s FUGUE
$ fugue -‐-‐loadfmap=fieldmap.nii -‐i epi.nii -‐-‐dwell=0.00059 -‐-‐unwarpdir=y -‐u unwarped_epi.nii
Echo spacing of EPIPhase encode direction
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How does this fit into my preprocessing pipeline?
UnwarpRaw EPI Motion Correct
Register to template
Concatenate XFMs
Concat. warp and XFM
(convertwarp)
Apply concat. warp and XFM (applywarp)
Make fieldmap
Final EPI
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Effect? It looks a little better.Original EPI Unwarped EPI
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Masking is important!Poorly maskedNicely masked