Dear FSL users,
We have acquired DWI data with a Philips 3T scanner. I would like to run eddy and DTIFIT on these data. Our scans are all in ‘fold-over direction = “AP”’, and we have 1 b0 and 30 dwi’s with ‘fat shift direction = “A” as well as 1 b0 and 30 dwi’s with ‘fat shift direction = “P”’. This should be equivalent to phase encoding directions A -> P and P -> A or vice versa.
However I’m unsure whether it is possible to combine all my data in one file before running eddy and DTIFIT. For now I have just used paste to combine the bvecs and bval files (for example: paste -d" " 2001210/*WIP*_A*.bval 2001210/*WIP*_P*.bval > 2001210/DTI_A_P.bval) and fslmerge to combine the nii files. I want to run eddy and DTIFIT with the following commands:
fsl_sub eddy --imain=DTI_A_P_1sliceless --mask=DTI_b0_brain_mask --index=index.txt --acqp=acqparams.txt --bvecs=DTI_A_P.bvec --bvals=DTI_A_P.bval --fwhm=0 --topup=topup_DTI_b0s --flm=quadratic --out=eddycor_DTI
fsl_sub dtifit -k eddycor_DTI -m DTI_b0_brain_mask -r DTI_A_P.bvec -b DTI_A_P.bval -o fitted_DTI
Would this be the right way of processing? Or should I process the set of images with ‘fat shift direction = “A”’ separately from those with ‘fat shift direction = “P”? Or is it possible to average both sets of scans (they have the same bvecs)?
Thank you in advance for any help or suggestions.
Kind regards,
Marjolein
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