biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/02/22 14:45] – old revision restored (2019/02/22 14:31) cmp12 | biac:analysis:topup_correction [2021/08/24 18:23] – cmp12 | ||
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There will be two series of single timepoint EPI images. | There will be two series of single timepoint EPI images. | ||
- | You need to calculate readout time in seconds ( 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 |
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) | ||
</ | </ | ||
+ | unfortunately at this point the polarity of the images will have to be determined from visual inspection. we aren't provided enough information in the metadata to give an entry into the BXH file ( yet ). | ||
+ | |||
+ | Here is a rough guide to help with inspection. | ||
+ | {{: | ||
- | the polarity for the entry will have to be determined from the **seriesdescription**, | ||
reverse will be " | reverse will be " | ||
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applytopup --imain=../ | applytopup --imain=../ | ||
applytopup --imain=../ | applytopup --imain=../ | ||
+ | </ | ||
+ | |||
+ | If you have the scenario where the functional data was acquired with acceleration, | ||
+ | |||
+ | < | ||
+ | echospacing in the BXH header is in microseconds | ||
</ | </ | ||
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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 | + | 2) 2 entire |
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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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 | ||
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< | < | ||
- | 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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< | < | ||
#concat the 2 series ( regular, reversed ) | #concat the 2 series ( regular, reversed ) | ||
- | bxh_concat | + | bxh_concat |
+ | 7_LAS.bxh bia6_00260_008_LAS.bxh both | ||
#extract the gradients | #extract the gradients | ||
- | extractdiffdirs --fsl both bvecs bvals | + | extractdiffdirs --fsl both.bxh bvecs bvals |
#convert to mif | #convert to mif | ||
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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 |
- | 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 | + | |
</ | </ | ||
biac/analysis/topup_correction.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1