Hi!

I am trying to bring my functional files to standard space (MNI) using the output from SSWarper. My understanding was that I could use the anat_WARP.nii file to bring my functional into standard space, but the result does not look aligned when I visualize it. Looking at a prior script I used with auto_warp.py instead of SSwarper, I had an "anat.un.aff.Xat.1D" file that I do not get with SSwarper (the auto_warp.py version of the functional in standard space looks aligned). I have attached my script using auto_warp.py (the one using SSwarper is identical except that the cat_matvec line does not contain the anat.un.aff.Xat.1D).

Is there a way for me to obtain the anat.un.aff.Xat.1D file from SSwarper? Or is there an alternative to it? Should I even be using 3dNwarpApply to bring my functional files to standard space if using SSwarper?


# for e2a: compute anat alignment transformation to EPI registration base
align_epi_anat.py -anat2epi -anat 001_mprage_ss+orig \
-suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-anat_has_skull no \
-AddEdge \
-volreg off -tshift off


foreach run ( $runs )
# register each volume to the base image
3dvolreg -verbose -zpad 4 -base vr_base_min_outlier+orig \
-1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run \
-cubic \
-1Dmatrix_save mat.r$run.vr.aff12.1D \
pb01.$subj.r$run.tshift+orig



# catenate volreg/epi2anat/tlrc xforms
cat_matvec -ONELINE \
anat.un.aff.Xat.1D \
001_mprage_ss_al_junk_mat.aff12.1D -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D


# apply catenated xform: volreg/epi2anat/tlrc/NLtlrc
# then apply non-linear standard-space warp
3dNwarpApply -master 001_mprage_ss+tlrc -dxyz 3 \
-source pb01.$subj.r$run.tshift+orig \
-nwarp "anat.un.aff.qw_WARP.nii mat.r$run.warp.aff12.1D" \
-prefix rm.epi.nomask.r$run

end