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!
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