failed alignment


I am running afni_proc but I am having an issue aligning my EPI to my T1. My datasets are very close that’s why I change the option -giant_move for big move and the results are better but still not good. I also tried with LPC+ZZ and is not different than the picture attached. Any suggestions? Here is my command
-subj_id 198_061814
-copy_anat /rcc/stor1/projects/GerDep/Luisa/Grief_V1/afni_proc/198_061814/anat/anatSS.ssWarp.nii
-anat_has_skull no
-dsets /rcc/stor1/projects/GerDep/Luisa/Grief_V1/afni_proc/198_061814/func/EPI_retroicor_fixed.nii
-blocks tshift align tlrc volreg blur mask scale regress
-radial_correlate_blocks tcat volreg
-tcat_remove_first_trs 5
-align_opts_aea -cost lpc -big_move -check_flip
-tlrc_base /rcc/stor1/projects/GerDep/Luisa/Grief_V1/afni_proc/MNI152_2009_template_SSW.nii.gz
-tlrc_NL_warped_dsets /rcc/stor1/projects/GerDep/Luisa/Grief_V1/afni_proc/198_061814/anat/anatQQ.ssWarp.nii
-volreg_align_to MIN_OUTLIER
-mask_epi_anat yes
-blur_size 4.0
-regress_stim_labels Face Shape
-regress_opts_3dD -jobs 2 -gltsym ‘SYM: Face -Shape’
-glt_label 1 F-S
-regress_censor_motion 0.3
-regress_censor_outliers 0.05
-regress_make_ideal_sum sum_ideal.1D
-regress_run_clustsim no
-html_review_style pythonic

There’s not much spatial contrast in your EPI data. Try changing the cost function to lpa, lpa+ZZ or nmi.

Daniel thank you so much! it improves A LOT but still not my favorite what do you think?

Here is what I used

-align_opts_aea -cost lpa+ZZ -big_move -check_flip

If you have pre-steady state data, then those might have better contrast, and you could use that as an external volreg_base_dset. Aside from that, you could try limiting the alignment to rigid body by adding “-rigid_body” to your “-align_opts_aea” options.

Daniel thank you so much for your help!

Yes I have pre-steady data, when you say “use that as an external volreg_base_dset” you are referring to change the epi_base to 1? (sorry if this is a dumb question)

================================= align ==================================

for e2a: compute anat alignment transformation to EPI registration base

(new anat will be current anatSS.ssWarp+orig) -anat2epi -anat anatSS.ssWarp+orig
-suffix _al_junk
-epi vr_base_min_outlier+orig -epi_base 1
-epi_strip 3dAutomask
-anat_has_skull no
-cost lpa+ZZ -rigid_body -big_move -check_flip
-volreg off -tshift off

I mean that option as an input to, so if you wanted to use the zeroth volume (AFNI starts counting with 0), then you could give this option along with all your other options:
-volreg_base_dset myepidset.nii.gz’[0]’

In that case, as with most cases, you would let fill in the epi_base itself.