Merge pull request #1468 from ANTsX/antsBrainExtractionReproMode

ENH: Make "-u" option also set a random seed for registration in antsBE

Scripts/antsBrainExtraction.sh

@@ -72,7 +72,10 @@ 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 (default), mhd
- -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 (1 (default)) 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
+ ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1.
  -k: Keep temporary files Keep brain extraction/segmentation warps, etc (default = false).
  -q: Use floating point precision Use antsRegistration with floating point precision.
 
@@ -286,6 +289,13 @@ else
  done
 fi
 
+if [[ ${USE_RANDOM_SEEDING} -eq 0 ]]; then
+ # Use random seed from Atropos unless one is already defined
+ if [[ -z $ANTS_RANDOM_SEED ]] ; then
+ export ANTS_RANDOM_SEED=19650218
+ fi
+fi
+
 ATROPOS_BRAIN_EXTRACTION_MRF="[ 0.1,1x1x1 ]"
 if [[ $DIMENSION -eq 2 ]];
  then