Hi there,

I have been trying to do an alignment with the following details:
- Anatomical to epi
- Partial coverage (I have a small epi slab centred over left SI)
- 7T data

I have two subjects, and things worked differently for the two. Only method 2 produced something that was not way, way off for sub2 where sub1 was generally ok with most methods (aside from method 3 & 5)



I have tried the following methods:

1. align_epi_anat.py, giant move (below)

2. align_epi_anat.py, ginormous move (as below but with ginormous)

align_epi_anat.py -anat2epi -anat FR_uniden_avg+orig \
-suffix _al_keep \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-epi2anat -giant_move -partial_coverage \
-volreg off -tshift off

3. align_epi_anat.py with lpc+ZZ cost function

align_epi_anat.py -anat2epi -anat FR_uniden_avg+orig \
-suffix _al_keep_lpcZZ \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-epi2anat -giant_move -partial_coverage \
-cost lpc+ZZ \
-volreg off -tshift off

4. zpad & nudge, then align_epi_anat.py

3dZeropad -I 0 -S 30 -A 0 -P 0 -L 0 -R 70 -prefix FR_uniden_avg_zpad FR_uniden_avg+orig
3drotate -quintic -clipit -rotate 0.00I 0.00R 0.00A -ashift 25.00S -45.00L 0.00P -prefix FR_uniden_zpad_nudged FR_uniden_avg_zpad+orig
3dZeropad -I -30 -S -30 -A 0 -P 0 -L -80 -R 0 -prefix FR_uniden_avg_zpad_nudged_zcor FR_uniden_zpad_nudged+orig

align_epi_anat.py -anat2epi -anat FR_uniden_avg_zpad_nudged_zcor+orig \
-suffix _al_keep_Ngiant \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-epi2anat -giant_move -partial_coverage \
-volreg off -tshift off

5. zpad & nudge, then 3dAllineate
3dAllineate \
-base vr_base_min_outlier+orig \
-input FR_uniden_avg_zpad_nudged_zcor+orig \
-prefix FR_uniden_avg_N3dA+orig \
-1Dmatrix_save FR_uniden_avg_N3dA_al_12.1D \
-cost lpc \
-final wsinc5 \
-source_automask -autoweight \
-twopass \
-verb


Any help on what I could try to improve these alignments would be very much appreciated!

Thank you,

Harriet