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biac:analysis:topup_correction

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biac:analysis:topup_correction [2019/02/21 19:29]
cmp12 		biac:analysis:topup_correction [2019/02/22 14:51]
cmp12
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 [[https://mrtrix.readthedocs.io/en/latest/|mrtrix3]] has a nice wrapper for FSL's eddy/topup/apply_topup that can do the above corrections and along with eddy corrections [[https://mrtrix.readthedocs.io/en/latest/|mrtrix3]] has a nice wrapper for FSL's eddy/topup/apply_topup that can do the above corrections and along with eddy corrections
 +
 +If you are running dwidenoise, do it BEFORE dwipreproc. 
  
 ==== Calculate your readout time ==== ==== Calculate your readout time ====
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 there are 2 scenarios that typically apply here there are 2 scenarios that typically apply here
-1) a short acquisition with RPE B0s +1) DWI and a short acquisition with RPE B0s 
-2) an entire acquisition with the same gradient table and reverse phase encoding +2) 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. In both scenarios it is important to create your data with normal phase encoding direction first, followed by reversed.
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 ==== Prepare your input datasets ==== ==== 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. For scenario 1, create your blip up / blip down B0 data the same way as above.
 <code> <code>
-bxhselect --timeselect 0 bia6_00197_012.bxh bu +bxhselect --timeselect 0 bi 
 +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
 +rm bu.* bd.*
 </code> </code>
  
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 #put THOSE back into the mif header #put THOSE back into the mif header
 mrconvert -grad grads.b dwi.mif dwi.mif -force mrconvert -grad grads.b dwi.mif dwi.mif -force
 +
 </code> </code>
  
-The last step seems redundant, but there is an issue with how mrtrix3 tools are handling the multi-shell GE data produced on our scanners.  If you data is NOT multi-shell, then you don't need it.  If your data IS multi-shell, then putting it back in can workaround other issues until their RC4 code is released.  +The last step seems redundant, but there is an issue with how mrtrix3 tools are handling the multi-shell GE data produced on our scanners.  If you data is NOT multi-shell, then you don't need it.  If your data IS multi-shell, then putting it back in can workaround other issues until their RC4 code is released.  [[https://github.com/MRtrix3/mrtrix3/issues/1487|discussion here]]
  
 ==== Run dwipreproc -rpe_pair ==== ==== Run dwipreproc -rpe_pair ====
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 <code> <code>
-dwipreproc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656  -debug+dwipre 
 +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 ) -rpe_pair specifies you're providing a pair of B0s ( regular, reversed )
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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 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 -pe_dir is the phase encode direction of your regular acquisition
 -readout_time from above   -readout_time from above  
 </code> </code>
  
 +
 +{{ :biac:analysis:trace_raw_corr.png?800 |}}
  
biac/analysis/topup_correction.txt · Last modified: 2023/02/23 18:43 (external edit)

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