Count only non-linear registrations as being complete, compliments tw…

…o-stage registration

bin/mb.sh

@@ -232,8 +232,8 @@ info "  $(echo ${subjects} | wc -w) subjects in input/subject"
 info "  $(echo ${models} | wc -w) models in input/models"
 
 info "Progress:"
-info "  $(find output/transforms/atlas-template -name '*0_GenericAffine.xfm' | wc -l) of $(( $(echo ${atlases} | wc -w) * $(echo ${templates} | wc -w) )) atlas-template registrations completed"
-info "  $(find output/transforms/template-subject -name '*0_GenericAffine.xfm' | wc -l) of $(( $(echo ${templates} | wc -w) * $(echo ${subjects} | wc -w) - $(echo ${templates} | wc -w) )) template-subject registrations completed"
+info "  $(find output/transforms/atlas-template -name '*1_NL.xfm' | wc -l) of $(( $(echo ${atlases} | wc -w) * $(echo ${templates} | wc -w) )) atlas-template registrations completed"
+info "  $(find output/transforms/template-subject -name '*1_NL.xfm' | wc -l) of $(( $(echo ${templates} | wc -w) * $(echo ${subjects} | wc -w) - $(echo ${templates} | wc -w) )) template-subject registrations completed"
 info "  $(find output/labels/candidates -type f | wc -l) of $(( $(echo ${atlases} | wc -w) * $(echo ${templates} | wc -w) * $(echo ${subjects} | wc -w) * $(echo ${labels} | wc -w) )) resample labels completed"
 info "  $(ls output/labels/majorityvote | wc -l) of $(( $(echo ${subjects} | wc -w) * $(echo ${labels} | wc -w) )) voted labels completed"
 if [[ -d output/multiatlas ]]