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biac:analysis:topup_correction [2019/09/04 17:45] cmp12 |
biac:analysis:topup_correction [2021/08/24 18:26] cmp12 |
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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/ | ||
+ | |||
+ | EffectiveEchoSpacing = TotalReadoutTime/ | ||
+ | |||
+ | 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. | ||
+ | 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 |
- | < | + | |
- | + | ||
- | echospacing in BXH header is in microseconds | + | |
- | </ | + | |
the regular B0s will get the " | the regular B0s will get the " | ||
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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 ==== |
- | < | + | |
- | + | ||
- | echospacing in BXH header is in microseconds | + | |
- | </ | + | |
==== Prepare your input datasets ==== | ==== Prepare your input datasets ==== | ||
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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. | ||
< | < | ||
- | 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 | 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 | ||
Line 245: | Line 252: | ||
< | < | ||
- | 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 ) | ||
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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 | + | - 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 | + | |
</ | </ | ||