Dear Jonathan,
>
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1610&L=FSL&P=R37920&1=FSL&9=A&J=on&X=CC99C9419E5E761F2D&Y=jonathan.repple%40googlemail.com&d=No+Match%3BMatch%3BMatches&z=4. We get the same error message after a while running eddy (segmentation error).
>
> A) Have you found a solution for that problem?
No. The problem is not trivial in that it is caused by a non-invertible fieldmap being fed into a software (eddy) that hinges on the field being invertible. There are ways to hack around it, but given that we anyway recommend using a topup field it hasn’t got the highest priority.
>
> B) Ben proposed using the fieldmap separately after running eddy without any fieldmap correction (see below).
> Would you recommend this strategy?
I think that is a sensible strategy. The critical part of that strategy (as always when using a “traditional fieldmap” in eddy) is the get the registration in step 3 just right. It is critical that this is very good.
>
> Ben's proposal:
>
> 1. Smooth the (prepared with fsl_prepare_fieldmap) fieldmap with fugue, using -s 4. Call this fieldmap_fugue
>
> 2. Use fugue to warp the magnitude image (brain extracted and eroded) based on the smoothed field map (--loadfmap=fieldmap_fugue) I use 0.0075 for dwell time because our protocol says “Echo spacing: 0.75ms.” Call this warped magnitude image FMM_bet_fugue
>
> 3. Use flirt (-dof 6) to generate a conversion matrix from fieldmap space to diffusion space. I flirt “in" FMM_bet_fugue and “ref” the brain extracted B0 image
>
> 4. Use flirt to apply this conversion matrix to fieldmap_fugue (from step 1). Call this fieldmap_fugue_dif
>
> 5. Use fugue to unwarp the eddy-corrected diffusion brain using --loadfmap=fieldmap_fugue_dif.
>
>
> C) Thanks for your help. A little more detailed information on what to do exactly with the output of the fsl_create_fieldmap command to incorporate that file in eddy on the eddy-userguide page, would be really helpful!
I will keep that in mind.
Jesper
>
> If you like me to upload the files, I am happy to do so!
>
> Best wishes,
>
> Jonathan
|