Hi Rick,

I am also having issues with my data not aligning correctly. I think I am missing a step but I cannot find anything on the message about it. I have taken the following steps:

APPROACH #1
1) Use FreeSurfer recon-all on my T1 image that has not been skull stripped or warped to MNI <-- is this problem?
2) Run @SUMA_Make_Spec_FS -sid Subject#
3) Run @SUMA_AlignToExperiment -exp_anat anat_final.101+tlrc. -surf_anat 101_SurfVol+orig.
- The anat_final.101_tlrc is aligned to all the epi data and warped to MNI space.

PROBLEM 1) 101_SurfVol+orig is in original space, which means that @SUMA_Make_Spec_FS is not using the native space images: the nonskullstripped original space images are displayed - which could because I used the T1 image --> Freesurfer. However, Freesurfer recon-all is skullstripping and warping into MNI. So, I am not sure what is wrong here.

APPROACH #2
1) Run step 1 and 2 above
2) Use align_epi_anat.py -anat2epi -anat 101_SurfVol+orig -anat_has_skull yes -save_skullstrip -suffix _al_junk -epi min_outlier_volume+orig -epi_base 0 -epi_strip 3dAutomask -volreg off -tshift off
- my epi data is aligned to the min_outlier. Here I am skullstripping and aligning the SurfVol to the min_outlier
3) @auto_tlrc -base /Users/sxa308/abin/MNI_avg152T1+tlrc -input 101_SurfVol_ns+orig -no_ss -init_xform AUTO_CENTER
- Now transfer the SurfVol_ns+orig to MNI space
4) Run @SUMA_AlignToExperiment

PROBLEM #2: The subject .spec file (101_both.spec) is not in MNI space and aligned to the min_outlier_volume.

QUESTION: Is there a way to convert and align the spec files? The only help I have found is your comment about: ConvertSurface has the -xmat_1D and -ixmat_1D options --> [afni.nimh.nih.gov]

APPROACH #3
1) Rerun recon-all (freesurfer) on my anat_final.101+tlrc
2) Then continue with approach #1 .... waiting on this.

Any insight or direction that you can provide would be fantastic!

Thanks,
Shana