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Dear all, I am trying to transform the Label file ( In this case Amygdala_Left hemisphere ) into functional space and i am encountering problems Following are the steps i have followed # Nonlinear transform highres to standard-where T1w.nii.gz is structural image 1. fnirt --in= T1w.nii.gz' --aff=reg/highres2standard.mat --cout=reg/highres2standard_warp --config=/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_2mm # Inverse of Non linear transform 2. inwarp --ref=T1w.nii.gz' --warp=reg/highres2standard_warp --out=reg/highres2standard_warp_inv # Now i am warping ROI ( Amygdala_L) to subject T1w.nii.gz space 3.applywarp --ref=T1w.nii.gz' --in=Amygdala_L.nii.gz --warp=reg/highres2standard_warp_inv --out=reg/Amygdala_L_Hres.nii.gz --interp=nn # Applying affine transform to move warped ROI (Amygdala_L_Hres.nii.gz) into functional space flirt -in reg/Amygdala_L_Hres.nii.gz -applyxfm -init reg/highres2example_func.mat -out Amygdala_L.nii.gz -datatype float -paddingsize 0.0 -interp nearestneighbour -ref reg/example_func.nii.gz and the result of this transformation is attached for your reference Could you please let me know why the ROI is completely misplaced here, and where i am doing wrong. Thanks Vasudev ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1