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biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/09/04 20:25] 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: | ||
| - | < | + | **For singleband images :** |
| + | < | ||
| + | readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/ | ||
| echospacing in the BXH header is in microseconds | echospacing in the BXH header is in microseconds | ||
| + | </ | ||
| + | |||
| + | |||
| + | **For mutli-band images the readout calculation is more complex: | ||
| + | < | ||
| + | readout = ( ( ceil ((1/ | ||
| + | |||
| + | AcquisitionMatrixPE = the acquisition size of the data ( acquisitionmatrix[0] ) | ||
| + | Round_factor = 4 if partial fourier ( PFF is in scanoptions ), 2 if full fourier. | ||
| + | Asset_R_factor = the reciprocal of the first value of dcm tag (0043,1083) | ||
| </ | </ | ||
| Line 97: | Line 110: | ||
| ==== 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 |
| - | < | + | |
| - | + | ||
| - | echospacing in BXH header is in microseconds | + | |
| - | </ | + | |
| the regular B0s will get the " | the regular B0s will get the " | ||
| Line 192: | 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 ==== |
| - | < | + | |
| - | + | ||
| - | echospacing in BXH header is in microseconds | + | |
| - | </ | + | |
| ==== Prepare your input datasets ==== | ==== Prepare your input datasets ==== | ||
| Line 244: | Line 249: | ||
| < | < | ||
| - | dwipre | + | dwifslpreproc |
| - | proc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656 | + | |
| -rpe_pair specifies you're providing a pair of B0s ( regular, reversed ) | -rpe_pair specifies you're providing a pair of B0s ( regular, reversed ) | ||
| Line 298: | Line 302: | ||
| 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 | + | - rpe_all signals that you've replicated |
| - | 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 | + | |
| </ | </ | ||
biac/analysis/topup_correction.1567628745.txt.gz · Last modified: 2019/09/04 20:25 by cmp12
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