biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/02/21 19:33] – [Prepare your input datasets] cmp12 | biac:analysis:topup_correction [2019/02/22 14:44] – cmp12 | ||
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The bottom two images are the mean functional image of a series uncorrected, | The bottom two images are the mean functional image of a series uncorrected, | ||
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If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info | If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info | ||
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If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info | If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info | ||
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==== Prepare your input datasets ==== | ==== Prepare your input datasets ==== | ||
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+ | Specify that a set of images (typically b=0 volumes) will be provided for use in inhomogeneity field estimation only | ||
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. | ||
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===== Scenario 2 ===== | ===== Scenario 2 ===== | ||
- | You have an entire acquisition with the same gradient table as your DWI sequence, but with reverse phase encoding. | + | You have an entire acquisition with the same gradient table as your DWI sequence, but with reverse phase encoding. This information will be used to perform a recombination of image volumes (each pair of volumes with the same b-vector but different phase encoding directions will be combined together into a single volume). |
Calculate the readout time in the same way as above | Calculate the readout time in the same way as above | ||
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dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug | dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug | ||
- | -rpe_all signals that you've replicated | + | -rpe_all signals that you've replicated |
+ | LL the directions with a rpe acquisition | ||
-pe_dir is the phase encode direction of your regular acquisition | -pe_dir is the phase encode direction of your regular acquisition | ||
-readout_time from above | -readout_time from above | ||
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biac/analysis/topup_correction.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1