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--- biac:analysis:topup_correction [2019/02/22 14:04] – cmp12
+++ biac:analysis:topup_correction [2019/02/22 17:41] – [Prepare your input datasets] cmp12
@@ Line 192: / Line 192: @@
 there are 2 scenarios that typically apply here
-) a short acquisition with RPE B0s
+) DWI and a short acquisition with RPE B0s
-) an entire acquisition with the same gradient table and reverse phase encoding
+) 2 entire acquisitions with the same gradient table and reverse phase encoding
 In both scenarios it is important to create your data with normal phase encoding direction first, followed by reversed.
@@ Line 264: / Line 264: @@
 <code>
 #concat the 2 series ( regular, reversed )
-bxh_concat bia6_00260_007_LAS.bxh bia6_00260_008_LAS.bxh both
+bxh_concat bia6_00260_00
+_LAS.bxh bia6_00260_008_LAS.bxh both
 #extract the gradients
-extractdiffdirs --fsl both bvecs bvals
+extractdiffdirs --fsl both.bxh bvecs bvals
 #convert to mif
@@ Line 289: / Line 290: @@
 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 |}}