Hi Daniel and Rick,

Thanks for the points.


Our situation is - we did the GLM and all the statistical analysis in FSL,
and now we want to average the funcitonals & anatomicals by using afni.

What I did is,
-I first deoblique the middle sub-brick of EPIs (example_func.nii) & register it to the skullstriped T1
-then used this matrix to align the z map (zstat.nii) to the skullstriped T1.
(go from middle volume of EPIs to T1 & then align z map with T1 by using this transform matrix)

I also swapped both the example_func & zstat to ASR at the very beginning.
Since they are from FSL which are in RPI.


Yes, I am still using 3dAllineate, since I want to use the output matrix (-1Dmatrix_save xxxx.1D) to apply to z map, to let them get aligned with T1.



---the command lines I used--------
3dSkullStrip -input ana1.nii -orig_vol -prefix ss_ana1
3dresample -prefix zstat_to_ASR -orient ASR -inset zstat.nii
3dWarp -oblique2card -prefix w.example_func example_func.nii
3dresample -prefix w.example_func_ASR -orient ASR -inset w.example_func+orig.HEAD
3dAllineate -base ss_ana1 -1Dmatrix_save MMM.1D -cost mi -input w.example_func_ASR
3dAllineate -master ss_ana1 -1Dmatrix_apply MMM.1D -input zstat_to_ASR -cost mi -prefix zstat_reg_to_ssana

Here are the attachment.

The w.example_func_ASR (EPI) aligns perfectly with anatomicals, but the resulting zstat_reg_to_ssana doesnt match well.

Is there anything I am missing?

Thanks a again

Jackie