AFNI version info (afni -ver
):
Hi experts, @ptaylor
I am struggling with normalizing my EPI to template space. I use afni_proc to do the normalization, and the QC file (HTML) shows the following anat (previously skull-stripped) to epi alignment:
It seems to be that the EPI extends somewhat beyond the anat (which again, is skullstripped).
The skull-stripped T1 to template space warp looks acceptable (?):
However, when I overlay the template on top of the final EPI (final_epi_vr_base_min_outlier+tlrc following normalization), the EPI extends outside the edge of the template:
I have tried tweaking the align_epi_anat options but that does not seem to help. Here are the relevant portions of the afni command I used:
afni_proc.py
-blocks despike tshift align tlrc volreg mask blur combine scale regress
-blur_size 6 -blur_in_mask yes
-copy_anat T1_bc_SS.nii.gz
-anat_has_skull no
-mask_epi_anat yes
-align_unifize_epi local
-align_opts_aea -cost lpc+ZZ -giant_move
-epi_strip 3dAutomask -check_flip
-tlrc_base MNI152_2009_template_SSW.nii.gz
-tlrc_NL_warp -tlrc_NL_warped_dsets
anatQQ.x.nii
anatQQ.x.aff12.1D
anatQQ.x_WARP.nii
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp
I tried using -epi_strip None but that didn't help.
I also tried looking at the ANAT -> template nonlinear transform separately (without looking just at the QC outputs) and it does look a bit weird :
template space overlayed in top of warper anatomical
The sswarper2 command I use for anat to template transform is:
sswarper2 \
-input T1_bc.nii.gz \
-subid x \
-base MNI152_2009_template_SSW.nii.gz \
-mask_ss T1_SS_mask.nii.gz \
-warpscale 0.5 \
-cost_nl_final pcl
and the 3dNwarpApply command I used to get the template-normalised anat is:
3dNwarpApply -master MNI152_2009_template_SSW.nii.gz
-source T1_bc_SS+orig.BRIK.gz
-nwarp "anatQQ.x_WARP.nii anatQQ.x.aff12.1D"
-prefix anat2mni
However, I might be doing something different from what sswarper2 does to generate the warped anatomical file, as that seems to perfectly overlap with the template.
Appreciate any tips on how to fix this.
Avi