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ANTsCT random seed #1541

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May 22, 2023
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ANTsCT random seed #1541

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c69ffc4
ENH: Set ANTS_RANDOM SEED if antsCorticalThickness.sh run with -u 0
cookpa May 22, 2023
da61ae5
DOC: Clarify random seeding option
cookpa May 22, 2023
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5 changes: 2 additions & 3 deletions Scripts/antsBrainExtraction.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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).
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18 changes: 14 additions & 4 deletions Scripts/antsCorticalThickness.sh
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Expand Up @@ -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
Expand Down Expand Up @@ -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).
Expand All @@ -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).

Expand All @@ -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
Expand Down Expand Up @@ -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:
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