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Hi Suraj, You have a MNI->T1 transform (MNI152_FNIRTed.nii.gz) and a T1->DWI transform (T1_in_DWI.mat), so you can combine them to get a MNI->DWI transform. So just set --warp1=MNI152_FNIRTed.nii.gz, and --postmat=T1_in_DWI.mat. Cheers, Paul On 09/01/2019, Suraj Thyagaraj <[log in to unmask]> wrote: > Paul, > > Thanks for your response. > > For the convertwarp usage with premat and postmat (convertwarp --ref=refvol > --premat=mat1 --warp1=vol1 --warp2=vol2 --postmat=mat2 --out=output_warp) > I'm not sure which files to pass as arguments. From the non-linear MNI->T1 > transformation, I have the affine transformation matrix (affine.mat), the > non-linear transformation image file (MNI152_FNIRTed.nii.gz) and the MNI > image to which the transformation has been applied using applywarp > (MNI_in_T1.nii.gz). From the linear T1->DWI, I have the transformation > matrix (T1_in_DWI.mat) and the transformed T1 image (T1_in_DWI.nii.gz). Any > pointers are much appreciated. As a reminder, the end goal is a > transformation from MNI to subject DWI space. > > Thanks, > Suraj > > ######################################################################## > > 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