recon-neonatal-cortex [-h] [-r WORK_DIR] [-c CONFIG] [-section SECTION]
-s SESSIONS [SESSIONS ...] [-b] [-w] [-cerebrum]
[-p] [-ensure-pial-is-outside-white-surface]
[-join-with-brainstem-and-cerebellum] [-nocut]
[-nocheck] [-keep-t1w-image] [-keep-t2w-image]
[-keep-regions-mask] [-f] [-v] [-d] [-t THREADS]
[-q QUEUE]


Reconstruct neonatal cortex from MR brain scan and Draw-EM segmentation

Command options

-h, --help

show this help message and exit

-r WORK_DIR, -root WORK_DIR, --root WORK_DIR, -work-dir WORK_DIR, --work-dir WORK_DIR

Root working directory

-c CONFIG, -config CONFIG, --config CONFIG

Optional custom configuration file

-section SECTION, --section SECTION

Configuration section name

-s SESSIONS [SESSIONS ...], -sessions SESSIONS [SESSIONS ...], --sessions SESSIONS [SESSIONS ...]

Either list of ‘{SubjectId}[-{SessionId}]’ strings or path of CSV file

-b, -brain, --brain

Reconstruct surface of brain mask

-w, -white, --white

Reconstruct white surface

-cerebrum, --cerebrum

Reconstruct/keep initial white surface

-p, -pial, --pial

Reconstruct pial surface

-ensure-pial-is-outside-white-surface, --ensure-pial-is-outside-white-surface

Ensure that pial surface is strictly outside the white surface

-join-with-internal-mesh, --join-with-internal-mesh

Join final mesh with internal (hemispheres) dividier mesh

-join-with-brainstem-and-cerebellum, --join-with-brainstem-and-cerebellum

Merge cerebrum surface mesh with brainstem and cerebellum surface mesh

-nocut, -nosplit, --nocut, --nosplit

Save individual (closed) genus-0 surfaces for each hemisphere

-nocheck, --nocheck

Disable consistency and self-intersection checks of (intermediate) surface meshes

-keep-t1w-image, --keep-t1w-image

Keep resampled T1-weighted image even when no -debug option given

-keep-t2w-image, --keep-t2w-image

Keep resampled T2-weighted image even when no -debug option given

-keep-regions-mask, --keep-regions-mask

Keep regions label image even when no -debug option given

-f, -force, --force

Overwrite existing output files

-v, -verbose, --verbose

Increase verbosity of output messages

-d, -debug, --debug

Keep/write debug output in temp_dir

-t THREADS, -threads THREADS, --threads THREADS

No. of cores to use for multi-threading

-q QUEUE, -queue QUEUE, --queue QUEUE

SLURM partition/queue