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antsRegistration reproducibility issues
Variance in output across multiple runs of the same registrations is a result of random sampling and floating point precision errors, as discussed below. These variances are usually small, and reflect uncertainty inherent to the registration method and to computation generally. We caution that a reproducible solution is not necessarily more accurate. However, some applications require complete reproducibility.
To meet this requirement, a "repro mode" has been added to the antsRegistrationSyN.sh and antsRegistrationSyNQuick.sh. This uses a fixed seed for the random number generation and uses reproducible metrics for registration. This should provide complete reproducibility, at the cost of computational time and possibly registration accuracy. Alternatively, a fixed seed and single-threaded execution will produce reproducible results.
Some registration methods in ITK, including global transforms (Rigid, Affine) randomly perturb the point set that is used to sample the registration metric in the virtual space. The point set is usually initialized to be a regular grid of points at the voxel centers of the fixed image. This might be downsampled randomly or regularly (ie, take every Nth point). Whenever downsampling is used, a random perturbation is applied to the chosen points to reduce bias in estimation. This appears to be the largest source of variance in registration results, according to the experiments described below.
The random perturbation can be made consistent between runs by setting the random seed, or disabled altogether by using dense sampling.
The SyN registration method was designed to use a densely sampled point set and does not apply any downsampling or perturbation to its sample points in versions prior to v2.4.3. In version v2.4.3, SyN allows other sampling strategies, but neither it nor BSplineSyN support user-defined seeds. That issue is now fixed.
In all scientific computing, the limited precision of floating point operations introduces variance that can be mitigated (often at the cost of performance), but usually not eliminated. Strategies such as compensated summation exist to manage precision errors.
Floating point precision may cause differences in the registration solution on the same images in several contexts including
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Multi-threading. The exact sequence of floating point operations can depend on the number of threads, as the results of computations performed in parallel are combined in an undefined order. The Mattes Mutual Information metric is affected by this, cross correlation is not.
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User choice of single or double precision for floating point operations.
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Differences in CPU architecture.
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Differences in compiler options for ANTs, ITK, or underlying system libraries.
Repro mode uses a fixed seed, and uses global correlation (GC) instead of mutual information for linear registration. While this is slower and possibly less robust than mutual information (MI), it is reproducible with multiple threads.
In antsRegistrationSyNQuick.sh, repro mode additionally changes the deformable metric from the default (MI) to cross correlation (CC). This will also increase computation time, which again can be mitigated by multi-threading.
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Set a fixed seed for randomization on the command line or by exporting the variable
ANTS_RANDOM_SEED. -
Disable multi-threading if using mutual information.
These two steps should provide reproducibility at the cost of increased computation time.
The variance in a simple registration task is mostly due to random point set sampling / perturbation in the rigid and affine stages. This can be removed by dense sampling or use of a fixed seed. Multi-threading and single vs double precision appear to have a small impact on average.
This was evaluated by running antsRegistrationSyNQuick.sh repeatedly on a set of 10 brains, and computing the pairwise overlap of brain labels between the different runs. Specifically, antsRegistrationSyNQuick.sh was called 25 times for each of 10 brain images, registering to a common template. The mean (over all subjects) Dice overlap of the cerebral white matter under different experimental conditions is listed below. Scripts and results for other brain regions are available here.
| Fixed Random Seed | Float precision | Threads | Mean Dice | SD Dice |
|---|---|---|---|---|
| TRUE | double | 1 | 1.000 | 0.000 |
| TRUE | single | 1 | 1.000 | 0.000 |
| TRUE | double | 2 | 0.993 | 0.005 |
| FALSE | double | 1 | 0.978 | 0.009 |
| FALSE | single | 1 | 0.979 | 0.008 |
| FALSE | single | 2 | 0.978 | 0.009 |
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Quick registration, may be less stable than
antsRegistrationSyN.sh(but much faster). -
The deformable stage uses SyN, so the variation in that stage only arises from multi-threading the Mutual Information metric.
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Overlap between runs measures reproducibility, not registration quality, so it does not address the question of whether using random sampling or double precision improves registration overall.