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--- biac:analysis:topup_correction [2019/09/04 15:50]
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+++ biac:analysis:topup_correction [2019/09/04 17:24]
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 unfortunately at this point the polarity of the images will have to be determined from visual inspection. we aren't provided enough information in the metadata to give an entry into the BXH file ( yet ).
-Here is a rough guide to help with inspection:
+Here is a rough guide to help with inspection.  Take note of the eyeballs being crushed in for AP and stretched out for PA.
 {{:biac:analysis:connneuro_func.png?800|}}
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 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
+</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.
+<code>readout = ((echospacing/sensefactor) * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6
+echospacing in the BXH header is in microseconds
 </code>

Brain Imaging & Analysis Center