Dear FSL users & team,
I have dwi data acquired with fieldmaps and I have written a script for eddy correction and distortion correction.
However, it seems to me that eddy is not introducing much correction, neither motion nor eddy currents, at least the effect is not too visible (unlike in the examples),
So I wanted to show here my script commands and the data I have in case you might provide me with some answers
(that is, either if my script is correct and I the images I get are within what is expected or whether I am doing something wrong)
Also as I understand eddy (the new version, not eddy_correct) includes motion correction. so it would be unnecessary to run mcflirt before, am I right? what is your recommendation?
My only doubt would be that as far as I understand, eddy does not do any gradient vector rotation to the images that are motion corrected.
If this is the case, wouldn't it be more correct to run mcflirt before and apply a rotation to each gradient corresponding to the transformation matrix of the corresponding volume, then running eddy?
I also include the fugue distortion correction command as some of the parameters are not completely clear and would like to confirm the numbers I am inputtign are the right ones given the scanning sequence properties.
I attach below a link to the dwi 4D data (original, after eddy command, and after fugue command) and a list of file contents and scanner parameters
Thanks in advance,
David
== dwi input/outputs:
https://app.box.com/s/tcuczkrw1xsoyzqxh6vtcm76wt4tbv0o
== input filenames:
dwi_or.nii.gz
gfm_mag.nii.gz
gfm_phase.nii.gz
== script:
eddy --imain=dwi_or.nii.gz --out=dwi_eddy.nii.gz --mask=brain_mask.nii.gz --bvecs=bvec.bvec --bvals=bval.bval --index=index.txt --acqp=acqparams.txt
bet gfm_mag.nii.gz gfm_mag_brain.nii.gz
fslmaths gfm_mag_brain.nii.gz -bin -ero gfm_mag_brain_mask.nii.gz
fslmaths gfm_phase.nii.gz -mas gfm_mag_brain_mask.nii.gz gfm_phase_brain.nii.gz
fslmaths gfm_phase_brain.nii.gz -div 4096 -mul 3.141592653589792 -div 0.00246 gfm_phase_radians.nii.gz -odt float
fugue --loadfmap=gfm_phase_radians.nii.gz --dwell=.00047500 --mask=gfm_mag_brain_mask.nii.gz -i dwi_eddy.nii.gz --unwarpdir=y- -u dwi_eddy_fugue.nii.gz
== index.txt:
1
===
== acqparams.txt:
0 -1 0 .05652500
===
== other parameters:
Read-out time: .05652500
echo spacing = 0.00095 # seconds in MS protocol time between echoes
accelration factor=2.
Effective echo spacing: .00047500
Echo Factor: 120
difference in fieldmap echo times = 0.00246 # seconds in SIEMENS
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