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biac:analysis:topup_correction [2021/08/24 16:04]
cmp12
biac:analysis:topup_correction [2023/02/23 18:43] (current)
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 You need to calculate readout time in seconds of the PEPOLAR images ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ). You need to calculate readout time in seconds of the PEPOLAR images ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ).
 +
  
 the readout time in seconds for the parameter file will be: the readout time in seconds for the parameter file will be:
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 +**For singleband images :** 
 +<code> 
 +readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 
  
 echospacing in the BXH header is in microseconds echospacing in the BXH header is in microseconds
 +</code>
 +
 +
 +**For mutli-band images the readout calculation is more complex:** 
 +<code>
 +readout = ( ( ceil ((1/Round_factor) * AcquisitionMatrixPE / Asset_R_factor ) * Round_factor) - 1 ) * EchoSpacing * 0.000001
 +
 +AcquisitionMatrixPE = the acquisition size of the data ( acquisitionmatrix[0] )
 +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> </code>
  
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 ==== Create your acq_params.txt file === ==== Create your acq_params.txt file ===
  
-the readout time in seconds for the parameter file will be: +calculate your readout time from above
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6  +
- +
-echospacing in BXH header is in microseconds +
-</code>+
  
 the regular B0s will get the "1" and the reverse phase B0s will get the "-1" the regular B0s will get the "1" and the reverse phase B0s will get the "-1"
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 If you are running dwidenoise, do it BEFORE dwipreproc.  If you are running dwidenoise, do it BEFORE dwipreproc. 
  
-==== Calculate your readout time ==== +==== Calculate your readout time as mentioned above ====
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6  +
- +
-echospacing in BXH header is in microseconds +
-</code>+
  
 ==== Prepare your input datasets ==== ==== Prepare your input datasets ====
biac/analysis/topup_correction.1629821047.txt.gz · Last modified: 2021/08/24 16:04 by cmp12