sct_deepseg_sc

Spinal Cord Segmentation using convolutional networks. Reference: Gros et al. Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks. Neuroimage. 2019 Jan 1;184:901-915.

usage: sct_deepseg_sc -i <file> -c {t1,t2,t2s,dwi} [-h]
                      [-centerline {svm,cnn,viewer,file}]
                      [-file_centerline <str>] [-thr <float>] [-brain {0,1}]
                      [-kernel {2d,3d}] [-ofolder <str>] [-o <file>] [-r {0,1}]
                      [-v <int>] [-qc <str>] [-qc-dataset <str>]
                      [-qc-subject <str>]

MANDATORY ARGUMENTS

-i

Input image. Example: t1.nii.gz

-c

Possible choices: t1, t2, t2s, dwi

Type of image contrast.

OPTIONAL ARGUMENTS

-centerline

Possible choices: svm, cnn, viewer, file

Method used for extracting the centerline:

  • svm: Automatic detection using Support Vector Machine algorithm.

  • cnn: Automatic detection using Convolutional Neural Network.

  • viewer: Semi-automatic detection using manual selection of a few points with an interactive viewer followed by regularization.

  • file: Use an existing centerline (use with flag -file_centerline)

Default: “svm”

-file_centerline

Input centerline file (to use with flag -centerline file). Example: t2_centerline_manual.nii.gz

-thr

Binarization threshold (between 0 and 1) to apply to the segmentation prediction. Set to -1 for no binarization (i.e. soft segmentation output). The default threshold is specific to each contrast and was estimated using an optimization algorithm. More details at: https://github.com/sct-pipeline/deepseg-threshold.

-brain

Possible choices: 0, 1

Indicate if the input image contains brain sections (to speed up segmentation). Only use with -centerline cnn. (default: 1 for T1/T2 contrasts, 0 for T2*/DWI contrasts)

-kernel

Possible choices: 2d, 3d

Choice of kernel shape for the CNN. Segmentation with 3D kernels is slower than with 2D kernels.

Default: “2d”

-ofolder

Output folder. Example: My_Output_Folder

Default: “/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/stable/documentation/source”

-o

Output filename. Example: spinal_seg.nii.gz

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1

-v

Possible choices: 0, 1, 2

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

Default: 1

-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