Steps to setup and apply FSL Topup correction on EPI data collected here with the use of your polarity images

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:

readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 

echospacing in the BXH header is in microseconds

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”

 echo '0 1 0 readout' > acq_params.txt
 echo '0 -1 0 readout' >> acq_params.txt

example output:
   0 1 0 0.077312
   0 -1 0 0.077312

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.

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

#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

inindex references the “regular” image index from your acq_params.txt file, which is the same phase encode direction of your functional runs

#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

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.

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

fslwrapbxh run008
mv run008.bxh tmp.bxh
bxh_merge ../bia6_00186_008_01.bxh tmp.bxh run008.bxh 
rm tmp.bxh

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.

the readout time in seconds for the parameter file will be:

readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 

echospacing in BXH header is in microseconds

the regular B0s will get the “1” and the reverse phase B0s will get the “-1”

 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:
   0 1 0 0.10656
   0 1 0 0.10656
   0 -1 0 0.10656
   0 -1 0 0.10656

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:

<datapoints label="diffusiondirection">
 <value>0 0 0</value>
 <value>0 0 0</value>
 <value>0.707107 0 0</value> <-- not a B0

Extract them with bxhselect:

bxhselect --timeselect 0:1 bia6_00197_012.bxh bu
bxhselect --timeselect 0:1 bia6_00197_013.bxh bd

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.

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

#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

inindex references the “regular” dwi B0s index from your acq_para ms. txt file

#apply it
applytopup --imain=bia6_00197_012.nii.gz --inindex=1 --method=jac --datain=acq_params.txt --topup=dwi_topup --out=dwi_corrected --verbose

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

fslwrapbxh dwi_corrected.nii.gz
mv dwi_corrected.bxh tmp.bxh
bxh_addgradients --fsl tmp.bxh bvecs bvals dwi_corrected.bxh
rm tmp.bxh

mrtrix3 has a nice wrapper for FSL's eddy/topup/apply_topup that can do the above corrections and along with eddy corrections

readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/100))) / 1e6 

echospacing in BXH header is in microseconds

there are 2 scenarios that typically apply here 1) a short acquisition with RPE B0s 2) an entire acquisition with the same gradient table and reverse phase encoding

For scenario 1, create your blip up / blip down B0 data the same way as above.

bxhselect --timeselect 0:1 bia6_00197_012.bxh bu 
bxhselect --timeselect 0:1 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 

#you can verify the table 
tesla:00414 cmp12$ mrinfo dwi.mif -dwgrad
          0           0           0           0
          0           0           0           0
          1           0           0        1500
   0.456784    0.889578           0     1501.42
  -0.264866    0.484757    0.833581     1501.51
   0.937268   -0.284081    0.202058     1499.14
  0.0630209   -0.806262    0.588192     1499.02
  -0.679047  -0.0940064     0.72805     1499.79
   0.686982    0.278993    0.670983     1500.08
  -0.232946    0.949777    0.208951      1500.7
   0.922569    0.178916    0.341841      1501.4
  -0.111021   -0.980188   -0.164032     1499.43
  -0.132016   -0.854107   -0.503064     1499.62