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biac:analysis:topup_correction

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biac:analysis:topup_correction [2021/08/24 18:23]
cmp12
biac:analysis:topup_correction [2021/08/24 18:29]
cmp12
Line 22: Line 22:
 <code> <code>
 readout = ( ( ceil ((1/Round_factor) * AcquisitionMatrixPE / Asset_R_factor ) * Round_factor) - 1 ) * EchoSpacing * 0.000001 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] ) 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 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) Asset_R_factor = the reciprocal of the first value of dcm tag (0043,1083)
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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"
Line 208: Line 201:
 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.txt · Last modified: 2021/08/24 18:29 by cmp12