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--- biac:analysis:topup_correction [2019/02/21 19:29]
cmp12
+++ biac:analysis:topup_correction [2023/02/23 18:43]
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-====== EPI Correction with polarity images using TOPUP ======
-Steps to setup and apply [[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide/|FSL Topup]] correction on EPI data collected here with the use of your polarity images
-==== Create your acquisition parameters ====
-There will be two series of single timepoint EPI images.  You can grab relevant info to create the acq_params.txt files from your XML header.
-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 ).
-the readout time in seconds for the parameter file will be:
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6
-echospacing in the BXH header is in microseconds
-</code>
-the polarity for the entry will have to be determined from the **seriesdescription**, which is typically "field map reverse polarity" or "field map regular"
-reverse will be "-1" in the acq_params.txt and regular will be "1"
-<code>
- echo '0 1 0 readout' > acq_params.txt
- echo '0 -1 0 readout' >> acq_params.txt
-example output:
-1 0 0.077312
--1 0 0.077312
-</code>
-==== Create your Blip Up/Down image ====
-Merge the two polarity images together into a 4D file with fsl_merge. Put them in the order of your acq_params.txt file.  In the example above, it would be regular, then reversed.
-<code>
-fslmerge -t bud ../bia6_00186_006.nii.gz ../bia6_00186_007.nii.gz
-tesla:00273 cmp12$ fslinfo bud.nii.gz
-    data_type      INT16
-    dim1           128
-    dim2           128
-    dim3           70
-    dim4           2
-</code>
-{{:biac:analysis:epi_polarity.png?800|}}
-==== Run topup to calculate the field and coefficients images for correction ====
-<code>
-#run popup calculate the field/coef
-topup --verbose --imain=bud --datain=acq_params.txt --config=$FSLDIR/src/topup/flirtsch/b02b0.cnf --out=rs_topup --fout=topup_field
-</code>
-==== Now apply the correction to your functional runs ====
-**inindex** references the "regular" image index from your acq_params.txt file, which is the same phase encode direction of your functional runs
-<code>
-#apply it
-applytopup --imain=../bia6_00186_008_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run008 --verbose
-applytopup --imain=../bia6_00186_009_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run009 --verbose
-applytopup --imain=../bia6_00186_010_01.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=rs_topup --out=run010 --verbose
-</code>
-The top two images are an example of the polarity images after correction, which is not necessary.
-The bottom two images are the mean functional image of a series uncorrected, then corrected by the topup results.
-{{:biac:analysis:epi_corrected.png?800|}}
-If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info
-<code>
-fslwrapbxh run008
-mv run008.bxh tmp.bxh
-bxh_merge ../bia6_00186_008_01.bxh tmp.bxh run008.bxh
-rm tmp.bxh
-</code>
----------------
-====== DWI Correction with RPE B0s using TOPUP ======
-Correcting DWI images using reverse phase encoded B0s is almost the same as the above.  Typically you'll have a couple B0s in your normal DWI acquisition, with a separate series of the same number of B0s collected with the phase encoding direction reversed.
-==== Create your acq_params.txt file ===
-the readout time in seconds for the parameter file will be:
-<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"
-<code>
- echo '0 1 0 [readout]' > acq_params.txt
- echo '0 1 0 [readout]' >> acq_params.txt
- echo '0 -1 0 [readout]' >> acq_params.txt
- echo '0 -1 0 [readout]' >> acq_params.txt
-example output:
-1 0 0.10656
-1 0 0.10656
--1 0 0.10656
--1 0 0.10656
-</code>
-==== Create your Blip Up/Down image ====
-First, you'll need to extract your B0s from the regular DWI acquisition.
-If you look at the gradient directions within the DWI acquisition the B0s will be "0 0 0".
-Within the BXH the first 2 directions are B0:
-<code>
-<datapoints label="diffusiondirection">
- <value>0 0 0</value>
- <value>0 0 0</value>
- <value>0.707107 0 0</value> <-- not a B0
-</code>
-Extract them with bxhselect:
-<code>
-bxhselect --timeselect 0:1 bia6_00197_012.bxh bu
-bxhselect --timeselect 0:1 bia6_00197_013.bxh bd
-</code>
-This will create bu.nii.gz / bd.nii.gz with the first 2 gradient directions ( the B0s )
-Now merge the extracted B0s from the regular acquisition with the images from the reversed acquisition.  Merge these in the same order of the acq_params.txt file.
-<code>
-fslmerge -t bud bu.nii.gz bd.nii.gz
-tesla:HCP cmp12$ fslinfo bud.nii.gz
-data_type      INT16
-dim1           256
-dim2           256
-dim3           92
-dim4           4
-</code>
-{{:biac:analysis:dwi_polarity.png?600|}}
-==== Run topup to calculate the field and coefficients images for correction ====
-<code>
-#run popup calculate the field/coef
-topup --verbose --imain=bud --datain=acq_params.txt --config=$FSLDIR/src/topup/flirtsch/b02b0.cnf --out=dwi_topup --fout=topup_field
-</code>
-==== Now apply the correction to your DWI ====
-**inindex** references the "regular" dwi B0s index from your acq_para
-ms.
-txt file
-<code>
-#apply it
-applytopup --imain=bia6_00197_012.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=dwi_topup --out=dwi_corrected --verbose
-</code>
-{{:biac:analysis:dwi_corrected.png?600|}}
-If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original info
-<code>
-fslwrapbxh dwi_corrected.nii.gz
-mv dwi_corrected.bxh tmp.bxh
-bxh_addgradients --fsl tmp.bxh bvecs bvals dwi_corrected.bxh
-rm tmp.bxh
-</code>
----------------
-====== DWI Correction with MRTRIX3 and RPE Data ======
-[[https://mrtrix.readthedocs.io/en/latest/|mrtrix3]] has a nice wrapper for FSL's eddy/topup/apply_topup that can do the above corrections and along with eddy corrections
-==== Calculate your readout time ====
-<code>readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6
-echospacing in BXH header is in microseconds
-</code>
-==== Prepare your input datasets ====
-there are 2 scenarios that typically apply here
-) a short acquisition with RPE B0s
-) an entire acquisition with the same gradient table and reverse phase encoding
-In both scenarios it is important to create your data with normal phase encoding direction first, followed by reversed.
-===== Scenario 1 =====
-==== Prepare your input datasets ====
-For scenario 1, create your blip up / blip down B0 data the same way as above.
-<code>
-bxhselect --timeselect 0 bia6_00197_012.bxh bu
-bxhselect --timeselect 0 bia6_00197_013.bxh bd
-fslmerge -t bud bu.nii.gz bd.nii.gz
-</code>
-Prepare your dwi series for input to mrtrix3.  If you use their mif data format, then the gradient tables will be automatically passed throughout their software with additional flags.
-<code>
-#pull the gradient table from BXH in FSL format
-extractdiffdirs --fsl bia6_00414_013.bxh bvecs bvals
-#convert nii.gz data into mif while inserting the gradients
-mrconvert -fslgrad bvecs bvals bia6_00414_013.nii.gz dwi.mif
-#export the table back out in their format
-mrinfo dwi.mif -export_grad_mrtrix grads.b
-#put THOSE back into the mif header
-mrconvert -grad grads.b dwi.mif dwi.mif -force
-</code>
-The last step seems redundant, but there is an issue with how mrtrix3 tools are handling the multi-shell GE data produced on our scanners.  If you data is NOT multi-shell, then you don't need it.  If your data IS multi-shell, then putting it back in can workaround other issues until their RC4 code is released.
-===== Run dwipreproc -rpe_pair =====
-Run [[https://mrtrix.readthedocs.io/en/latest/reference/scripts/dwipreproc.html|dwipreproc]] with the "-rpe_pair" option
-<code>
-dwipreproc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656  -debug
--rpe_pair specifies you're providing a pair of B0s ( regular, reversed )
--se_epi is you bud image
--pe_dir is your dwi's phase encode direction
--readout_time is from calculation above
-</code>
-dwipreproc will run topup, eddy and apply topup.  eddy will output update diffusion directions and insert them into your dwi_corr.mif output header.
-You can generate a BXH header for a mif file with:
-<code>
-mif2bxh dwi_corr.mif dwi_corr.bxh
-</code>
-===== Scenario 2 =====
-You have an entire acquisition with the same gradient table as your DWI sequence, but with reverse phase encoding.
-Calculate the readout time in the same way as above
-==== Prepare your input datasets ====
-This time you'll concatenate the 2 DWI acquisitions.  regular, then reversed
-<code>
-#concat the 2 series ( regular, reversed )
-bxh_concat bia6_00260_007_LAS.bxh bia6_00260_008_LAS.bxh both
-#extract the gradients
-extractdiffdirs --fsl both bvecs bvals
-#convert to mif
-mrconvert -fslgrad bvecs bvals both.nii.gz dwi.mif
-#re-extract table
-mrinfo dwi.mif -export_grad_mrtrix grads.b
-#put corrected table back in
-mrconvert -grad grads.b dwi.mif dwi.mif -force
-#remove the temporary files ( bvecs, bvals, both.* )
-</code>
-==== Run dwipreproc -rpe_all ====
-Run dwipreproc with the "-rpe_all" option
-<code>
-dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug
--rpe_all signals that you've replicated ALL the directions with a rpe acquisition
--pe_dir is the phase encode direction of your regular acquisition
--readout_time from above
-</code>

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