biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/09/04 15:50] – cmp12 | biac:analysis:topup_correction [2019/09/04 20:25] – cmp12 | ||
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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 ). | 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. Below shows the PEPOLAR images in red/blue on top of a mean functional. |
{{: | {{: | ||
- | |||
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applytopup --imain=../ | applytopup --imain=../ | ||
applytopup --imain=../ | applytopup --imain=../ | ||
+ | </ | ||
+ | |||
+ | If you have the scenario where the functional data was acquired with acceleration, | ||
+ | |||
+ | < | ||
+ | echospacing in the BXH header is in microseconds | ||
</ | </ | ||
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For scenario 1, create your blip up / blip down B0 data the same way as above. | For scenario 1, create your blip up / blip down B0 data the same way as above. | ||
< | < | ||
- | 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 | bxhselect --timeselect 0 bia6_00197_013.bxh bd | ||
fslmerge -t bud bu.nii.gz bd.nii.gz | fslmerge -t bud bu.nii.gz bd.nii.gz |
biac/analysis/topup_correction.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1