Hi Rick,

I've tried the steps you described above, but the alignment seems to be similar as before.

[MPIB7193-R-52c:~/Desktop/Neuer_Ordner ] jackie% 3dAttribute IJK_TO_DICOM_REAL run1+orig.

-4 0 0 124 0 4 0 -140.7606 0 0 4.6 -9.560291

[MPIB7193-R-52c:~/Desktop/Neuer_Ordner ] jackie% 3dWarp -oblique2card -prefix card_run1 run1+orig


[MPIB7193-R-52c:~/Desktop/Neuer_Ordner ] jackie% 3dWarp -oblique_parent run1+orig -prefix oblique_ana1 ana1+orig

Here are the images attached.

I checked the raw data with mri_info (Freesurfer),
the slice orientation of ana.nii is sagittal, that of run.nii is axial.
They are not oblique.

One more difference is the overlay of Fun1/ run1 onto anatomicals.
run1+orig seems to match a bit better then Fun1+orig

Fun1+orig was created by--

3dWarp -matvec_in2out example_fun2highres.mat -fsl_matvec -gridset oblique_ana1+orig -prefix Fun1 zstat1+orig

(I've also tried the other way around, 'deoblique' the EPIs, but the alignment is still a bit dismatched)

cheers,

Jackie