Here is the output from the 3dinfo command:
-108.727364 91.842567 -74.730621 3.000000 3.000000 3.000000 RPI pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_forallineate.nii.gz
-109.027374 92.142578 -74.430626 2.400000 2.400000 2.400000 RPI pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz
I should also clarify that the command I sent you was one I did for just testing out the banding, which is why I had the same input and base (I was just keeping it simple). The actual original command from my script that caused the banding was this:
3dAllineate \
-overwrite \
-base mprage.noskull_at.nii.gz \
-input pb01.${sub}.r${run}.e${echo}.tcat.nii.gz \
-1Dmatrix_apply pb01.${sub}.r${run}.e${echo}.tcat.XFM.EPI2EPI2MPR2ATL_motionINT_EPIxEPI1.aff12.1D \
-mast_dxyz 3 \
-prefix pb01.${sub}.r${run}.e${echo}.tcat.atlas_motionINT_EPIxEPI1.nii.gz
I also reran 3dAllineate using -master (code below) and the image still had bands:
3dAllineate -overwrite -base pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz -master pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_forallineate.nii.gz -input pb01.MOV008_20180330.r01.e1.tcat.2NEW.nii.gz -1Dmatrix_apply pb01.MOV008_20180330.r01.e1.tcat.2NEW.motion_REF-EPI1.aff12.1D -prefix pb01.MOV008_20180330.r01.e1.tcat.2NEW.REF-EPI1_allineate_forcedresample_withmaster.nii.gz
Thanks!
Ben
