Thank you for your reply.
One more follow up question to all DTI experts:
It has been suggested that averaging the two volumes is better for SNR than concatenating them:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1105&L=FSL&D=0&P=30679
However, the opposite has also been suggested:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;bde7018a.1407
How do I determine what the best approach is for my analyses?
Kind regards,
Marjolein
On Fri, 20 Feb 2015 16:15:09 +0000, Vasilis M. Karlaftis <[log in to unmask]> wrote:
>Dear Janna Marie,
>
>I am not an expert but these processing steps seem fine to me; I am also
>using them for my analysis. I think that in Stam's link
><http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt1/index.html#eddy>
>it
>says exactly what you have to do for 2 blips.
>Just be sure that your index and acqparams files have the correct values,
>e.g. all A volumes have 1 and P volumes have 2 in index; and your acqparams
>file has 0 -1 0 "dwell time" in first row and 0 1 0 "dwell time" in second
>row.
>
>I would also suggest to include the --sse option when running dtifit, if
>you aim to evaluate the DT model at some point.
>
>Best regards,
>Vasilis
>
>On 20 February 2015 at 12:37, Janna Marie Hoogendam <[log in to unmask]
>> wrote:
>
>> 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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