Hi,
I'm not exactly sure what's causing the problems here, but there are two strong candidates:
1) The orientation of your images look very different. Try running fslreorient2std on all of your images prior to the analysis and then repeat the analysis you've been doing. That may well help.
2) Check the parameters that you are entering into topup and epi_reg. It is possible to use the wrong parameters in topup but still get good output from topup for everything except the fieldmap. It is the fieldmap where the timing parameters really matter (they cancel out within topup for its own corrections). So if you use the wrong value there then you fieldmap will be scaled incorrectly and this will give bad distortion correction. The same thing happens if you use the wrong value for the echospacing in epi_reg. I see from here that you are using 53.46 millisecond and that is a *lot*. Most EPI sequences have echo spacings in a range more like 0.3 - 5 milliseconds, so I would double check this value. Note that in topup the timing parameter requested is *not* the same as in epi_reg. The echo spacing in epi_reg is the time per line in k-space, whereas topup wants the total readout time.
I hope this helps.
All the best,
Mark
> On 19 Mar 2018, at 20:24, SUBSCRIBE FSL Erik <[log in to unmask]> wrote:
>
> Hi Team
> I am having some struggles with applying topup field maps to fMRI data using epi_reg.
>
> I ran topup using two spin echo DTI B0 images as such:
> topup --imain=$USER_SCRATCH/subjects/${subject}/dti/both_b0 --datain=$USER_SCRATCH/subjects/${subject}/dti/my_acq_param.txt --config=b02b0.cnf --out=$USER_SCRATCH/subjects/${subject}/dti/my_topup_results --fout=$USER_SCRATCH/subjects/${subject}/fmap
>
> Next, I multiplied the --fout file by 2*pi:
> fslmaths $USER_SCRATCH/subjects/${subject}/fmap -mul 6.28319 $USER_SCRATCH/subjects/${subject}/fmap_rads
>
> Then ran epi_reg using the resultant map on my BOLD data acquired with RL phase encode direction with the fmapmag and fmapmagbrain images as B0 images from the DTI series with and without skull:
> epi_reg --epi=$USER_SCRATCH/subjects/input/${subject}/BOLD_RL_e1.nii.gz --t1=$USER_SCRATCH/subjects/${subject}/mri/nu.nii --t1brain=$USER_SCRATCH/subjects/${subject}/mri/brain.nii --out=$USER_SCRATCH/subjects/${subject}/e1_to_struct_RL --fmap=$USER_SCRATCH/subjects/${subject}/fmap_rads --fmapmag=$USER_SCRATCH/subjects/${subject}/dti/hifib0 --fmapmagbrain=$USER_SCRATCH/subjects/${subject}/dti/fmap_brain --echospacing=0.05346 --pedir=x
>
> Lastly, I used applywarp on the original BOLD series:
> applywarp -i $USER_SCRATCH/subjects/${subject}/BOLD_RL_e1_test -r $USER_SCRATCH/MNI152_T1_2mm_brain.nii.gz -w $USER_SCRATCH/subjects/${subject}/e1_to_struct_warp.nii.gz -o $USER_SCRATCH/subjects/${subject}/func_warped_RL_e1.nii.gz
>
> To my limited experience, the fmap image and the warp image from epi_reg look how I might expect; however, the applywarp step clearly goes wrong and the output looks nothing like a brain! I am not certain where this is going wrong, but have not had success modifying these steps so far. Any help would be appreciated. Thanks!
>
>
> <fmaprads.png><warp.png><func_warped.png>
|