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fix wmparc mapped #116

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Mar 14, 2022
Merged

fix wmparc mapped #116

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17 changes: 11 additions & 6 deletions recon_surf/recon-surf.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -811,16 +811,21 @@ echo " " |& tee -a $LF
RunIt "$cmd" $LF
popd


# 18 sec hyporelabel run whatever else can be done without sphere, cortical ribbon and segmentations
# 18 sec hyporelabel (generate aseg.presurf.hypos.mgz from aseg.presurf and ?h.white)
cmd="recon-all -s $subject -hyporelabel $fsthreads"
RunIt "$cmd" $LF
fi

# 55sec mapping aparc.mapped back to volume (should be a nicer aparc+aseg compared to input, due to surface help)???
cmd="mri_aparc2aseg --s $subject --volmask --aseg aseg.presurf.hypos --annot aparc.mapped --o $mdir/aparc.mapped+aseg.mgz "
RunIt "$cmd" $LF

# 4sec creating an aseg from the aparc.mapped+aseg.mgz (should be better than the aseg.presurf.hypos..)
# generate aparc.mapped+aseg.mgz, needed later to paint-in white matter labels also
# 55sec mapping aparc.mapped back to volume (could be a nicer aparc+aseg compared to input, due to surface help, not verified yet)
cmd="mri_aparc2aseg --s $subject --volmask --aseg aseg.presurf.hypos --annot aparc.mapped --o $mdir/aparc.mapped+aseg.mgz"
RunIt "$cmd" $LF


if [ "$fsaparc" == "0" ] ; then

# 4sec creating an aseg from the aparc.mapped+aseg.mgz (instead of aseg.presurf.hypos..)
# we call it aseg, because that is needed below in recon-all segstats
cmd="apas2aseg --i $mdir/aparc.mapped+aseg.mgz --o $mdir/aseg.mgz "
RunIt "$cmd" $LF
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