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--- biac:analysis:topup_correction [2019/02/22 14:03] – cmp12
+++ biac:analysis:topup_correction [2019/02/22 14:44] – cmp12
@@ Line 67: / Line 67: @@
 The bottom two images are the mean functional image of a series uncorrected, then corrected by the topup results.
-{{:biac:analysis:epi_corrected.png?800|}}
+{{ :biac:analysis:epi_corrected.png?800|}}
 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
@@ Line 163: / Line 163: @@
 </code>
-{{:biac:analysis:dwi_corrected.png?600|}}
+{{ :biac:analysis:dwi_corrected.png?600|}}
 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
@@ Line 200: / Line 200: @@
 ==== Prepare your input datasets ====
+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.
@@ Line 287: / Line 289: @@
 dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug
--rpe_all signals that you've replicated ALL the directions with a rpe acquisition
+-rpe_all signals that you've replicated A
+LL the directions with a rpe acquisition
 -pe_dir is the phase encode direction of your regular acquisition
 -readout_time from above
 </code>
+{{ :biac:analysis:trace_raw_corr.png?800 |}}