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--- biac:analysis:topup_correction [2019/09/04 17:24]
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+++ biac:analysis:topup_correction [2019/09/04 20:25]
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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.  Take note of the eyeballs being crushed in for AP and stretched out for PA.
+Here is a rough guide to help with inspection.  Take note of the eyeballs being crushed in for AP and stretched out for PA.  Below shows the PEPOLAR images in red/blue on top of a mean functional.
 {{:biac:analysis:connneuro_func.png?800|}}
@@ Line 214: / Line 214: @@
 For scenario 1, create your blip up / blip down B0 data the same way as above.
 <code>
-bxhselect --timeselect 0 bi
+bxhselect --timeselect 0 bia6_00197_012.bxh bu
-a6_00197_012.bxh bu
 bxhselect --timeselect 0 bia6_00197_013.bxh bd
 fslmerge -t bud bu.nii.gz bd.nii.gz

Brain Imaging & Analysis Center