Dear Ben, Dear Jesper,
we are running into the same kind of problem with our DTI data (same issue: only Siemens fieldmap, no reverse phase encoding). We get the same error message after a while running eddy (segmentation error).
A) Ben proposed using the fieldmap separately after running eddy without any fieldmap correction (see below).
Would you recommend this strategy?
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.
B) Also, I noticed that in Ben's original code, he did not report to use the field_mat option in eddy. When we try to incorporate the .mat-file created in Ben's first FLIRT-step (flirt -in <FMM_BET_ero> -ref <NoDiffBet> -omat <fieldmap2dif.mat>) in our eddy calculation, we get an error message that the file does not contain a rigid transformation. The matfile itsself looks okay:
1.017922091 0.008996027587 -0.006016609064 -3.750376717
-0.007675637977 1.045219252 -0.01051661839 -4.681491907
0.001407249022 0.01309824726 1.028790877 -4.956612221
0 0 0 1
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!
If you like me to upload the files, I am happy to do so!
Best wishes,
Jonathan
|