Hi there,

I am trying to align my SurfVol to my experimental anatomy but I just can't get it to fit well enough. This is despite me nudging the SurfVol for a long time and getting it very close to the experimental anatomy.

The imaged I attached is as good as I can get (underlay: experimental anatomical (aligned to epi); overlay: SurfVol (aligned to experimental anatomy))

Background: The experimental anatomy has been aligned to my epi data (7T, partial FOV/ slab). I made my own whole brain anatomy (full field of view) with skull using 3dAllineate as afni_proc.py gives you a skull-free partial FOV anatomical when you align it to partial epi data.

To improve alignment, my colleague suggested to use a SurfVol with the skull on, but I can't see any options in @SUMA_Make_Spec to allow this. Is this possible?

I also saw in this (https://afni.nimh.nih.gov/pub/dist/edu/latest/suma/suma.pdf) that one option if your alignment to experiment fails is to use 3dTagalign but I can't quite work out what options I need.

I was also wondering if I could use 3dAllineate with the transformation matrix I used to align my experimental anatomy with the epi data in some way?

I have pasted my code below. Any help would be very much appreciated.

Note: the -wd flag always makes it much worse, makes SurfVol big and warped

Step 1. Creating whole-brain warped experimental anatomical

## Create full coverage, skull on, warped anatomical
3dZeropad -I 100 -S 100 -A 100 -P 100 -L 50 -R 120 \
-prefix rm.{$raw_anat_name}_wholebrain_padded+orig \
$raw_anat_dir/{$raw_anat_name}{$raw_anat_ext}

# gunzip rm.{$raw_anat_name}_wholebrain_padded+orig.BRIK.gz

3dAllineate -source rm.{$raw_anat_name}_wholebrain_padded+orig \
-final wsinc5 \
-1Dmatrix_apply $mat_dir/$mat_name \
-prefix rm.{$raw_anat_name}_wholebrain_padded_warped+orig

# gunzip rm.{$raw_anat_name}_wholebrain_padded_warped+orig.BRIK.gz

# Remove excess
3dZeropad -I -0 -S -0 -A -180 -P -60 -L -200 -R -0 \
-prefix {$raw_anat_name}_wholebrain_unpad_warped+orig \
rm.{$raw_anat_name}_wholebrain_padded_warped+orig


Step 2. Align SurfVol to experimental anatomy

# Zeropad SurfVol
3dZeropad -I 20 -S 20 -A 20 -P 20 -L 0 -R 100 \
-prefix rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded \
rm.{$surf_subj_num}_{$subj_init}_SurfVol+orig

# Then open it and nudge it towards the location of the anatomical

# Create a nudged surfvol in the experimental folder
3drotate -quintic -clipit -rotate 6.47I 7.64R 35.43A -ashift -3.45S -81.29L -16.76P -prefix rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded_nudged rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded+orig

# Make transformation matrix
cat_matvec 'rm.'{$surf_subj_num}'_'{$subj_init}'_SurfVol_padded_nudged+orig::ROTATE_MATVEC_000000' -I \
> XFORM0.1D

# Use this nudged surfvol to create the surfvol aligned to experiment in next step



# ======================= surf (map data to surface) =======================
# map EPI data to the surface domain

# align the surface anatomy with the current experiment anatomy
@SUMA_AlignToExperiment \
-init_xform XFORM0.1D -align_centers \
-surf_anat rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded+orig \
-exp_anat $exp_anat \
-prefix {$subj}_SurfVol_Alnd_Exp_xform2


Other Step 2 attempts that did not work either

#### wd flag
# @SUMA_AlignToExperiment -exp_anat $exp_anat \
# -surf_anat rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded_nudged2+orig \
# -align_centers \
# -wd -EA_clip_below -80 \
# -atlas_followers -overwrite_resp S \
# -prefix {$subj}_SurfVol_Alnd_Exp_wd_EAclip

#### Basic version
# Removed -align_centres
# @SUMA_AlignToExperiment -exp_anat $exp_anat \
# -surf_anat rm.{$surf_subj_num}_{$subj_init}_SurfVol_unpadded_nudged2+orig \
# -atlas_followers -overwrite_resp S \
# -prefix {$subj}_SurfVol_Alnd_Exp_2_unpad_no_al_centres

#### Old commands generated by afni_proc - don't work
# @SUMA_AlignToExperiment -exp_anat $exp_anat \
# -surf_anat $surface_dir/P0{$surf_subj_num}_{$subj_init}_SurfVol+orig \
# -wd -strip_skull surf_anat \
# -atlas_followers -overwrite_resp S \
# -prefix ${surf_subj_num}_SurfVol_Alnd_Exp