Dear Daniel,
are those FA images? It is not really possible to say anything by just looking at the FA images. At what stage do those holes appear? Are they present in all volumes after running eddy?
Jesper
> On 19 Nov 2018, at 15:51, Daniel Callow <[log in to unmask]> wrote:
>
> 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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> <FA_101.Rest_fmap2.png>
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