Hello, I have been trying to apply a field map to my eddy correction, however when doing so my data seems to get worse. Specifically when using the field map there are these large artifacts of missing data like in the attached image.
below is my field map creation script....
fsl_prepare_fieldmap SIEMENS /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/phase_map*.nii /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/*eroded.nii.gz /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/fmap_rads.nii 2.46
flirt -dof 6 -in /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/skull_strip_avg_mag_eroded_reoriented.nii.gz -ref /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4_reorient.nii.gz -out /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti -omat /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/alfmap2dti.mat
flirt -in /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/fmap_rads_Hz_reoriented.nii.gz -ref /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4_reorient.nii.gz -init /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/alfmap2dti.mat -applyxfm -out /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti
fslmaths /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti.nii.gz -kernel gauss 0.8493290 -fmean /Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti_smoothed.nii.gz
and eddy script....
eddy --imain=/Volumes/DANIEL/${subj}/${subj}.${cond}/DTI_analysis.nii.gz --mask=/Volumes/DANIEL/${subj}/${subj}.${cond}/COPY_b0_brain_0.4_mask_eroded.nii.gz --acqp=acqp.txt --index=index.txt --bvecs=bvec.txt --bvals=bvalue.txt --repol --field=/Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti_smoothed --out=eddy_corrected_data
Any ideas what might be causing these artifacts to occur?
Best,
Daniel
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