Dear all,
Maybe this question escaped your attention, but we (Marjolein and myself) would be very pleased to hear your reaction to the issue raised below.
Thanks in advance,
best wishes,
Janna Marie
> Op 11 feb. 2015, om 10:33 heeft M Barendse <[log in to unmask]> het volgende geschreven:
>
> 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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