From c69ffc4d52011d50dfbfb9335ae5d0aabab6814e Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Mon, 22 May 2023 09:34:06 -0400
Subject: [PATCH 1/2] ENH: Set ANTS_RANDOM SEED if antsCorticalThickness.sh run
 with -u 0

Previously, this only set the random seed for antsAtroposN4.sh
---
 Scripts/antsCorticalThickness.sh | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/Scripts/antsCorticalThickness.sh b/Scripts/antsCorticalThickness.sh
index ee4f7a489..a772d08fe 100755
--- a/Scripts/antsCorticalThickness.sh
+++ b/Scripts/antsCorticalThickness.sh
@@ -76,7 +76,7 @@ We use *label* to denote a label image with values in range 0 to N.
                                                     * Registration metric mask (-f)
                                                     * Thickness prior image (-r).
 
-     -m:  Brain extraction probability mask     Brain *probability* mask in the segmentation template space. A binary mask 
+     -m:  Brain extraction probability mask     Brain *probability* mask in the segmentation template space. A binary mask
                                                 is an acceptable probability image.
 
      -p:  Brain segmentation priors             Tissue *probability* priors corresponding to the image specified
@@ -127,7 +127,7 @@ Optional arguments:
                                                 https://github.com/ANTsX/ANTs/wiki.
 
      -f:  extraction registration mask          Binary metric mask defined in the segmentation template space (-e). During the
-                                                registration for brain extraction, the similarity metric is only computed within 
+                                                registration for brain extraction, the similarity metric is only computed within
                                                 this mask.
 
      -k:  keep temporary files                  Keep brain extraction/segmentation warps, etc (default = 0).
@@ -147,7 +147,10 @@ Optional arguments:
 
      -j:  use floating-point precision          Use single float precision in registrations (default = 0).
 
-     -u:  use random seeding                    Use random number generated from system clock in Atropos (default = 1).
+     -u:  use random seeding                    Use random number generated from system clock (default = 1). If 0, a fixed
+                                                random seed is used. To set your own seed, set this option to 0 and export the
+                                                environment variable ANTS_RANDOM_SEED. To achieve exactly identical results, you must
+                                                also set ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS to 1.
 
      -v:  use b-spline smoothing                Use B-spline SyN for registrations and B-spline exponential mapping in DiReCT (default = 0).
 
@@ -173,7 +176,7 @@ Optional arguments:
                                                 Another example would be computing cortical thickness in the presence
                                                 of white matter lesions. We can accommodate this by specifying a lesion mask
                                                 posterior as an additional posterior (suppose label '7'), combining this with
-                                                normal white matter in the thickness estimation by specifying '-c "WM[ 7 ]"' 
+                                                normal white matter in the thickness estimation by specifying '-c "WM[ 7 ]"'
                                                 or '-c "3[ 7 ]"'.
 
      -q:  Use quick registration parameters     If = 1, use antsRegistrationSyNQuick.sh as the basis for registration
@@ -540,6 +543,13 @@ if [[ $DEBUG_MODE -gt 0 ]];
 
   fi
 
+if [[ ${USE_RANDOM_SEEDING} -eq 0 ]]; then
+  # Use fixed random seed unless one is already defined
+  if [[ -z $ANTS_RANDOM_SEED ]] ; then
+    export ANTS_RANDOM_SEED=19650218
+  fi
+fi
+
 ################################################################################
 #
 # Preliminaries:

From da61ae5abecec5258ad8f7129aef835d747cd9c8 Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Mon, 22 May 2023 09:48:13 -0400
Subject: [PATCH 2/2] DOC: Clarify random seeding option

---
 Scripts/antsBrainExtraction.sh | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/Scripts/antsBrainExtraction.sh b/Scripts/antsBrainExtraction.sh
index 3f44c6edf..588b1a564 100755
--- a/Scripts/antsBrainExtraction.sh
+++ b/Scripts/antsBrainExtraction.sh
@@ -131,9 +131,8 @@ Optional arguments:
                                                 Without this option, this script calls antsAI to search for a good initial moving
                                                 transform.
      -s:  Image file suffix                     Any of the standard ITK IO formats e.g. nrrd, nii.gz, mhd (default = $OUTPUT_SUFFIX)
-     -u:  Use random seeding                    Use random number generated from system clock (1) or a fixed seed (0). Using
-                                                "-u 0" overrides a system setting of ANTS_RANDOM_SEED. To produce identical results,
-                                                multi-threading must also be disabled by setting the environment variable
+     -u:  Use random seeding                    Use random number generated from system clock (1) or a fixed seed (0). To produce identical
+                                                results, multi-threading must also be disabled by setting the environment variable
                                                 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1. Default = $USE_RANDOM_SEEDING.
      -k:  Keep temporary files                  Keep brain extraction/segmentation warps, etc (default = $KEEP_TMP_IMAGES).
      -q:  Use single floating point precision   Use antsRegistration with single (1) or double (0) floating point precision (default = $USE_FLOAT_PRECISION).