Dear Stam,
Thanks for your reaction. We have read the documentation, but did not find information about combining two maps, one acquired in A-P, the other in P-A direction.
We have done the following:
- combined the bvecs and the bval files (for example: paste -d" " 2001210/*WIP*_A*.bval 2001210/*WIP*_P*.bval > 2001210/DTI_A_P.bval) for the two directions
- used fslmerge to combine the nii files
- ran topup
- performed eddy using these command:
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
- performed dtifit
fsl_sub dtifit -k eddycor_DTI -m DTI_b0_brain_mask -r DTI_A_P.bvec -b DTI_A_P.bval -o fitted_DTI
Is this the correct way to combine the AP and PA maps?
Thanks a lot,
Marjolein and Janna Marie
> Op 20 feb. 2015, om 13:21 heeft Stamatios Sotiropoulos <[log in to unmask]> het volgende geschreven:
>
> Dear Janna
>
> You first need to run topup and then eddy, to correct for susceptibility-induced and then eddy current-induced distortions. There is extensive documentation on how to do that on the FSL webpage, but also practicals from the FSL course that walk you through both steps. See for instance:
>
> http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt1/index.html
>
> Hope this helps
> Stam
>
>
> On 20 Feb 2015, at 12:08, Janna Marie Hoogendam <[log in to unmask]> wrote:
>
>> 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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