sct_deepseg_gm

Spinal Cord Gray Matter (GM) Segmentation using deep dilated convolutions. The contrast of the input image must be similar to a T2*-weighted image: WM dark, GM bright and CSF bright. Reference: Perone CS, Calabrese E, Cohen-Adad J. Spinal cord gray matter segmentation using deep dilated convolutions. Sci Rep 2018;8(1):5966.

usage: sct_deepseg_gm -i <file> [-o <file>] [-m {large,challenge}]
                      [-thr <float>] [-t] [-qc <str>] [-qc-dataset <str>]
                      [-qc-subject <str>] [-h] [-v <int>]
                      [-profile-time [<file>]] [-trace-memory [<folder>]]

MANDATORY ARGUMENTS

-i

Image filename to segment (3D volume). Example: t2s.nii.gz.

OPTIONAL ARGUMENTS

-o

Output segmentation file name. Example: sc_gm_seg.nii.gz

-m

Possible choices: large, challenge

Model to use (large or challenge). The model ‘large’ will be slower but will yield better results. The model ‘challenge’ was built using data from the following challenge: goo.gl/h4AVar.

Default: “large”

-thr

Threshold to apply in the segmentation predictions, use 0 (zero) to disable it.

Default: 0.999

-t

Enable TTA (test-time augmentation). Better results, but takes more time and provides non-deterministic results.

MISC ARGUMENTS

-qc

The path where the quality control generated content will be saved.

-qc-dataset

If provided, this string will be mentioned in the QC report as the dataset the process was run on

-qc-subject

If provided, this string will be mentioned in the QC report as the subject the process was run on

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

Default: 1

-profile-time

Enables time-based profiling of the program, dumping the results to the specified file.

If no file is specified, human-readable results are placed into a ‘time_profiling_results.txt’ document in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/7.0/documentation/source’). If the specified file is a .prof file, the file will instead be in binary format, ready for use with common post-profiler utilities (such as snakeviz).

-trace-memory

Enables memory tracing of the program.

When active, a measure of the peak memory (in KiB) will be output to the file peak_memory.txt. Optionally, developers can also modify the SCT code to add additional snapshot_memory() calls. These calls will ‘snapshot’ the memory usage at that moment, saving the memory trace at that point into a second file (memory_snapshots.txt).

By default, both outputs will be placed in the current directory (’/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/7.0/documentation/source’). Optionally, you may provide an alternative directory (-trace-memory <dir_name>), in which case all files will be placed in that directory instead. Note that this WILL incur an overhead to runtime, so it is generally advised that you do not run this in conjunction with the time profiler or in time-sensitive contexts.