construct-atlas¶

Synopsis¶

construct-atlas [-h] [-a MEANS [MEANS ...]] [-s SIGMA [SIGMA ...]]
[-o OUTDIR] [-w TMPDIR] [-e ENERGY]
[-c CHANNELS [CHANNELS ...]]
[-m MEASURES [MEASURES ...]] [-b BENDING [BENDING ...]]
[--bins BINS] [--window WINDOW]
[--spacing SPACING [SPACING ...]]
[-j JACOBIAN [JACOBIAN ...]] [--bch-terms BCHTERMS]
[-g GROWTH] [-i START] [-n STEPS] [-q LONGQUEUE]
[--short-queue SHORTQUEUE] [-t THREADS] [-v VERBOSE]
config

Description¶

Construct (spatio-temporal) atlas from images of the same anatomy of different subjects. To construct a spatio-temporal atlas, images of subjects at different ages spread over the atlas time range are required. Please cite the following preprint when you use this command in your research (or the respective peer-reviewed article when accepted): Schuh et al., “Unbiased construction of a temporally consistent morphological atlas of neonatal brain development”, bioRxiv, 2018. doi:10.1101/251512

Arguments¶

config¶: JSON file with atlas configuration.

Command options¶

-h, --help¶: show this help message and exit

-a MEANS [MEANS ...], --ages MEANS [MEANS ...], --means MEANS [MEANS ...]¶: Discrete time points for which to construct atlas.

-s SIGMA [SIGMA ...], --sigma SIGMA [SIGMA ...]¶: Standard deviation of temporal kernel(s).

-o OUTDIR, --output OUTDIR, --outdir OUTDIR¶: Output directory of final atlas.

-w TMPDIR, --workdir TMPDIR, --tmpdir TMPDIR¶: Working directory for intermediate files.

-e ENERGY, --energy ENERGY¶: Energy function of image registration (e.g., ‘asym’, sym’, ‘ic’).

-c CHANNELS [CHANNELS ...], --channels CHANNELS [CHANNELS ...]¶: Images to use for multi-channel registration.

-m MEASURES [MEASURES ...], --measures MEASURES [MEASURES ...]¶: Image (dis-)similarity measure to use for each channel.

-b BENDING [BENDING ...], --bending BENDING [BENDING ...]¶: Bending energy weight for each step.

--bins BINS¶: No. of bins to use for histogram-based measures.

--window WINDOW¶: Local window size for NCC measure in voxels.

--spacing SPACING [SPACING ...]¶: Control point spacing for each step.

-j JACOBIAN [JACOBIAN ...], --jacobian JACOBIAN [JACOBIAN ...]¶: Jacobian penalty weight for each step.

--bch-terms BCHTERMS No. of BCH terms to use for composition of SV FFDs.¶

-g GROWTH, --growth GROWTH¶: Whether to joinedly estimate mean shape and change.

-i START, --start START¶: Continue construction after the specified step.

-n STEPS, --steps STEPS¶: Number of steps of iterative atlas construction/refinement. Use ‘iterations’ config entry if not specified (default: 10).

-q LONGQUEUE, --queue LONGQUEUE, --long-queue LONGQUEUE¶: Name of batch system queue. Use ‘condor’ for HTCondor. Otherwise, the argument is assumed to be the name of a SLURM partition.

--short-queue SHORTQUEUE¶: Name of batch system queue to use for short running jobs (about 1-30 min). Use –long-queue by default.

-t THREADS, --threads THREADS¶: Maximum number of CPU cores/threads to use.

-v VERBOSE, --verbose VERBOSE¶: Verbosity level of output messages: 0) no output, 1) report progress, 2) print command arguments.