Thanks Steven. That really helped me refine my steps. My commands I ended up using are as follows in case anyone else is every interested in the answer that resolved this question. Thanks again everyone for your help!
fsl_reg ${subj}.DWI2DT_FA.nii /usr/local/fsl/data/standard/FMRIB58_FA_1mm.nii.gz ${subj}.DWI2DT_FA.MNI-fsl-reg.nii -FA
convert_xfm -omat ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii.mat -inverse ${subj}.DWI2DT_FA.MNI-fsl-reg.nii.mat
invwarp -w ${subj}.DWI2DT_FA.MNI-fsl-reg.nii_warp.nii.gz -o ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii_warp.nii.gz -r ${subj}.DWI2DT_FA.nii
applywarp -i /usr/local/fsl/data/atlases/JHU/JHU-WhiteMatter-labels-2mm.nii.gz -o ${subj}.JHU_to_FA_Native -r ${subj}.DWI2DT_FA.nii -w ${subj}.FMRIB58_to_FA_Native-fsl-reg.nii_warp.nii.gz -d float -s --superlevel=a --interp=nn
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