What's the differences between antsRegistrationSyNQuick.sh and antsRegistrationSyN.sh?

[WangRoss]

I am confused what's the differences between antsRegistrationSyNQuick.sh and antsRegistrationSyN.sh? Why is it quicker using antsRegistrationSyNQuick.sh than antsRegistrationSyN.sh? Is it related with 'repro' mode?

Thank you!

[cookpa]

It's unrelated to repro mode, which is available in both scripts. The speed difference is for two main reasons: a faster metric (Mutual Information in quick instead of Cross Correlation) and fewer iterations. I believe the quick script does not do any iterations at full resolution.

Both scripts will print the actual antsRegistration command before running it, so you can see exactly what is being done.

[gdevenyi]

The complete differences in the script:

--- /opt/quarantine/ANTs/bin/antsRegistrationSyN.sh     2020-06-18 10:17:13.000000000 -0400
+++ /opt/quarantine/ANTs/bin/antsRegistrationSyNQuick.sh        2020-06-18 10:17:13.000000000 -0400
@@ -76,7 +76,7 @@
         br: rigid + deformable b-spline syn (2 stages)
         bo: deformable b-spline syn only (1 stage)
 
-     -r:  radius for cross correlation metric used during SyN stage (default = 4)
+     -r:  histogram bins for mutual information in SyN stage (default = 32)
 
      -s:  spline distance for deformable B-spline SyN transform (default = 26)
 
@@ -156,7 +156,7 @@
         br: rigid + deformable b-spline syn (2 stages)
         bo: deformable b-spline syn only (1 stage)
 
-     -r:  radius for cross correlation metric used during SyN stage (default = 4)
+     -r:  histogram bins for mutual information in SyN stage (default = 32)
 
      -s:  spline distance for deformable B-spline SyN transform (default = 26)
 
@@ -228,7 +228,7 @@
  Number of threads:        $NUMBEROFTHREADS
  Spline distance:          $SPLINEDISTANCE
  Transform type:           $TRANSFORMTYPE
- CC radius:                $CCRADIUS
+ MI histogram bins:        $NUMBEROFBINS
  Precision:                $PRECISIONTYPE
  Use histogram matching    $USEHISTOGRAMMATCHING
 ======================================================================================
@@ -280,7 +280,7 @@
 SPLINEDISTANCE=26
 TRANSFORMTYPE='s'
 PRECISIONTYPE='d'
-CCRADIUS=4
+NUMBEROFBINS=32
 MASKIMAGES=()
 USEHISTOGRAMMATCHING=0
 COLLAPSEOUTPUTTRANSFORMS=1
@@ -296,7 +296,7 @@
    ;;
       d)  # dimensions
    DIM=$OPTARG
-   ;; 
+   ;;
       e)  # seed
    RANDOMSEED=$OPTARG
    ;;
@@ -325,7 +325,7 @@
    PRECISIONTYPE=$OPTARG
    ;;
       r)  # cc radius
-   CCRADIUS=$OPTARG
+   NUMBEROFBINS=$OPTARG
    ;;
       s)  # spline distance
    SPLINEDISTANCE=$OPTARG
@@ -394,15 +394,15 @@
 ORIGINALNUMBEROFTHREADS=${ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS}
 
 # NUMBEROFTHREADS is > 0 if the option has been set to a positive value
-if [[ $NUMBEROFTHREADS -lt 1 ]]; 
+if [[ $NUMBEROFTHREADS -lt 1 ]]
   then
     # Number of threads not set on the command line, try ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
-    if [[ $ORIGINALNUMBEROFTHREADS -gt 0 ]]; 
+    if [[ $ORIGINALNUMBEROFTHREADS -gt 0 ]]
       then
        NUMBEROFTHREADS=$ORIGINALNUMBEROFTHREADS
-      else
+    else
        NUMBEROFTHREADS=1
-      fi
+    fi
   fi
 
 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$NUMBEROFTHREADS
@@ -444,29 +444,29 @@
 #
 ##############################
 
-RIGIDCONVERGENCE="[ 1000x500x250x100,1e-6,10 ]"
+RIGIDCONVERGENCE="[ 1000x500x250x0,1e-6,10 ]"
 RIGIDSHRINKFACTORS="8x4x2x1"
 RIGIDSMOOTHINGSIGMAS="3x2x1x0vox"
 
-AFFINECONVERGENCE="[ 1000x500x250x100,1e-6,10 ]"
+AFFINECONVERGENCE="[ 1000x500x250x0,1e-6,10 ]"
 AFFINESHRINKFACTORS="8x4x2x1"
 AFFINESMOOTHINGSIGMAS="3x2x1x0vox"
 
-SYNCONVERGENCE="[ 100x70x50x20,1e-6,10 ]"
+SYNCONVERGENCE="[ 100x70x50x0,1e-6,10 ]"
 SYNSHRINKFACTORS="8x4x2x1"
 SYNSMOOTHINGSIGMAS="3x2x1x0vox"
 
 if [[ $ISLARGEIMAGE -eq 1 ]];
   then
-    RIGIDCONVERGENCE="[ 1000x500x250x100,1e-6,10 ]"
+    RIGIDCONVERGENCE="[ 1000x500x250x0,1e-6,10 ]"
     RIGIDSHRINKFACTORS="12x8x4x2"
     RIGIDSMOOTHINGSIGMAS="4x3x2x1vox"
 
-    AFFINECONVERGENCE="[ 1000x500x250x100,1e-6,10 ]"
+    AFFINECONVERGENCE="[ 1000x500x250x0,1e-6,10 ]"
     AFFINESHRINKFACTORS="12x8x4x2"
     AFFINESMOOTHINGSIGMAS="4x3x2x1vox"
 
-    SYNCONVERGENCE="[ 100x100x70x50x20,1e-6,10 ]"
+    SYNCONVERGENCE="[ 100x100x70x50x0,1e-6,10 ]"
     SYNSHRINKFACTORS="10x6x4x2x1"
     SYNSMOOTHINGSIGMAS="5x3x2x1x0vox"
   fi
@@ -502,7 +502,7 @@
 SYNMETRICS=''
 for(( i=0; i<${#FIXEDIMAGES[@]}; i++ ))
   do
-    SYNMETRICS="$SYNMETRICS --metric CC[ ${FIXEDIMAGES[$i]},${MOVINGIMAGES[$i]},1,${CCRADIUS} ]"
+    SYNMETRICS="$SYNMETRICS --metric MI[ ${FIXEDIMAGES[$i]},${MOVINGIMAGES[$i]},1,${NUMBEROFBINS}]"
   done
 
 SYNSTAGE="${SYNMETRICS} \
@@ -512,7 +512,7 @@
 
 if [[ $TRANSFORMTYPE == 'sr' ]] || [[ $TRANSFORMTYPE == 'br' ]];
   then
-    SYNCONVERGENCE="[ 50x20,1e-6,10 ]"
+    SYNCONVERGENCE="[ 50x0,1e-6,10 ]"
     SYNSHRINKFACTORS="2x1"
     SYNSMOOTHINGSIGMAS="1x0vox"
           SYNSTAGE="${SYNMETRICS} \