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Hi Vasudev, Your initial structural-to-standard linear registration has failed spectacularly. I would suggest removing the neck from your structural image (using robustfov) and brain-extracting it (using bet) before running flirt. It is also essential to check the results of every step, as even though a command may not print any errors, it may not have produced good results. Cheers, Paul On Wed, 21 Aug 2019 at 22:37, Dev vasu <[log in to unmask]> wrote: > 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 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1