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test_ST_04132023
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test_ST_04132023
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for w in {0,0.001,0.01,0.1,1};do
out=/Users/qm022/output_dynamic_shim_${w}_sequentialslice
mkdir ${out}
st_b0shim dynamic --coil /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/coil_profiles/profiles_7T_rewrite_header.nii \
/Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/coil_profiles/jason_coil_config.json \
--fmap /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_fieldmap/fieldmap.nii.gz \
--anat /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_fieldmap/fieldmap.nii.gz \
--mask /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_mask/magnitude_bet_mask.nii.gz \
--mask-dilation-kernel-size 3 --optimizer-criteria grad --regularization-factor 0.1 \
--optimizer-method least_squares --slices sequential --scanner-coil-order -1 \
--output-file-format-coil slicewise-ch --output-value-format delta \
--output ${out} --epi_echo_time 0.025 --weighting-signal-loss ${w}
out=/Users/qm022/output_dynamic_shim_${w}_volumeslice
mkdir ${out}
st_b0shim dynamic --coil /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/coil_profiles/profiles_7T_rewrite_header.nii \
/Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/coil_profiles/jason_coil_config.json \
--fmap /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_fieldmap/fieldmap.nii.gz \
--anat /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_fieldmap/fieldmap.nii.gz \
--mask /Users/qm022/Documents/shimming-toolbox/examples/sub-20220622/output_mask/magnitude_bet_mask.nii.gz \
--mask-dilation-kernel-size 3 --optimizer-criteria grad --regularization-factor 0.1 \
--optimizer-method least_squares --slices volume --scanner-coil-order -1 \
--output-file-format-coil slicewise-ch --output-value-format delta \
--output ${out} --epi_echo_time 0.025 --weighting-signal-loss ${w}
done