biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/09/04 17:18] cmp12 |
biac:analysis:topup_correction [2019/09/04 17:24] cmp12 |
applytopup --imain=../bia6_00186_009_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run009 --verbose | applytopup --imain=../bia6_00186_009_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run009 --verbose |
applytopup --imain=../bia6_00186_010_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run010 --verbose | applytopup --imain=../bia6_00186_010_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run010 --verbose |
| </code> |
| |
| If you have the scenario where the functional data was acquired with acceleration, but the PEPOLAR images were not. You can create an additional acq_params file with a modified readout time to help prevent over correction. You will need to divide the echospacing by the sensefactor from your BXH header of the functional run. If your functional data and PEPOLAR images have the same sensefactor, this compensation is not needed. |
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| <code>readout = ((echospacing/sensefactor) * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 |
| echospacing in the BXH header is in microseconds |
</code> | </code> |
| |
biac/analysis/topup_correction.txt · Last modified: 2023/02/23 18:43 (external edit)