Paul,
Hi. Thank you very much for your help. I hope your trip went well.
I ran the code below. The results are odd to me because the region masks are larger than they should be and have values [0-1].
Sincerely,
Dante
# estimate warp
3dQwarp \
-source /usr/local/apps/afni/current/linux_centos_7_64/MNI152_2009_template_SSW.nii.gz"[0]" \
-base /usr/local/apps/afni/current/linux_centos_7_64/TT_N27_SSW.nii.gz"[0]" \
-prefix dset_mni_in_tlrc.nii \
-lpa \
-allineate \
-allineate_opts "-twopass"
# apply_warp
for InputFile in $(ls AAN_*_MNI152_1mm_v1p0_20150630.nii) ; do
new=${InputFile/_MNI152_1mm_v1p0_20150630.nii/}
3dNwarpApply \
-nwarp dset_mni_in_tlrc_WARP.nii \
-master /usr/local/apps/afni/current/linux_centos_7_64/TT_N27_SSW.nii.gz"[0]" \
-prefix "$new"_tlrc.nii \
-source "$InputFile"
3drefit \
-space TLRC \
-view tlrc \
"$new"_tlrc.nii
done
