Differences

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--- biac:analysis:topup_correction [2019/09/04 17:45] – cmp12
+++ biac:analysis:topup_correction [2021/08/24 18:22] – cmp12
@@ Line 10: / Line 10: @@
 the readout time in seconds for the parameter file will be:
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6
+<code>
+**For singleband images :**
+readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6
 echospacing in the BXH header is in microseconds
+**For mutli-band images the readout calculation is more complex:**
+readout = ( ( ceil ((1/Round_factor) * AcquisitionMatrixPE / Asset_R_factor ) * Round_factor) - 1 ) * EchoSpacing * 0.000001
+EffectiveEchoSpacing = TotalReadoutTime/ (reconMatrixPE - 1)
+AcquisitionMatrixPE = the acquisition size of the data ( acquisitionmatrix[0] )
+reconMatrixPE = the size of the reconstructed data ( may be different from acquisition because of FFT rules )
+Round_factor = 4 if partial fourier ( PFF is in scanoptions ), 2 if full fourier.  most all scans will be 4
+Asset_R_factor = the reciprocal of the first value of dcm tag (0043,1083)
 </code>
@@ Line 214: / Line 228: @@
 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
@@ Line 245: / Line 258: @@
 <code>
-dwipre
+dwifslpreproc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656  -debug
-proc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656  -debug
 -rpe_pair specifies you're providing a pair of B0s ( regular, reversed )
@@ Line 299: / Line 311: @@
 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 ALL the directions with a rpe acquisition
-A
+- pe_dir is the phase encode direction of your regular acquisition
-LL the directions with a rpe acquisition
+- readout_time from above
--pe_dir is the phase encode direction of your regular acquisition
--readout_time from above
 </code>