I am trying to rotate a brain image (T1) according to a rigid body transformation rule XXX.mat (4x4 matrix). To do so, I used the folllowing fsl flirt command:
/usr/local/fsl/bin/flirt \
-in /Users/eunmi/Desktop/QSIPREP/CHA_crash_subjects/sub-200087/anat/sub-200087_T1w.nii.gz \
-applyxfm -init /Users/eunmi/Desktop/QSIPREP/CHA_crash_subjects/sub-200087/anat/xform.mat \
-out /Users/eunmi/Desktop/QSIPREP/CHA_crash_subjects/sub-200087/anat/sub-200087_T1w_REALINGED.nii.gz \
-paddingsize 0.0 -interp trilinear \
-ref /Users/eunmi/Desktop/QSIPREP/CHA_crash_subjects/sub-200087/anat/sub-200087_T1w.nii.gz
However, the output image was cropped like the picture below :
Could anyone tell me what I did wrong? Any help would be greatly appreciated!