For some reason, the registration between EPI and anatomical goes poorly for one of my participants and I can't seem to resolve this problem. My flip angle is 90 and, following recommendations elsewhere on this message board, I have tried nmi and lpa (and several other) cost functions. I've also tried using a two-step -big_move option. Nevertheless, my EPI PFC seems warped beyond the MPRAGE anatomical extents. Are there any other options I should try?

Using afni_proc.py, followed by a few minor modifications, I come up with the following bits of code for alignment:
# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, anat_mprage_skullstripped_ns+orig)
align_epi_anat.py -anat2epi -anat anat_mprage_skullstripped+orig \
-save_skullstrip -suffix _al_junk \
-epi pb01.$subj.r01.card+orig -epi_base 1 \
-epi_strip 3dAutomask \
-cost nmi \
-volreg off -tshift off -deoblique on

and for volume registration:
# ================================= volreg =================================
# align each dset to base volume, align to anat, warp to tlrc space
# *** changed $subj.r$run.tshift+orig to $subj.r$run.card+orig ***

# verify that we have a +tlrc warp dataset
if ( ! -f anat_mprage_skullstripped+tlrc.HEAD ) then
echo "** missing +tlrc warp dataset: anat_mprage_skullstripped+tlrc.HEAD"
exit
endif

# register and warp
foreach run ( $runs )
# register each volume to the base
3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.card+orig'[2]' \
-1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \
-cubic \
-1Dmatrix_save mat.r$run.vr.aff12.1D \
pb01.$subj.r$run.card+orig

# create an all-1 dataset to mask the extents of the warp
3dcalc -overwrite -a pb01.$subj.r$run.card+orig -expr 1 \
-prefix rm.epi.all1

# catenate volreg, epi2anat and tlrc transformations
cat_matvec -ONELINE \
anat_mprage_skullstripped+tlrc::WARP_DATA -I \
anat_mprage_skullstripped_al_junk_mat.aff12.1D -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D

# apply catenated xform : volreg, epi2anat and tlrc
3dAllineate -base anat_mprage_skullstripped+tlrc \
-input pb01.$subj.r$run.card+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 4 \
-cost nmi \
-prefix rm.epi.nomask.r$run

# warp the all-1 dataset for extents masking
3dAllineate -base anat_mprage_skullstripped+tlrc \
-input rm.epi.all1+orig \
-1Dmatrix_apply mat.r$run.warp.aff12.1D \
-mast_dxyz 4 -final NN -quiet \
-cost nmi \
-prefix rm.epi.1.r$run

# make an extents intersection mask of this run
3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc
end



Edited 1 time(s). Last edit at 10/18/2015 04:59PM by westbrok.