sct_label_utils

Utility functions for label images.

usage: sct_label_utils -i <file> [-o <file>] [-ilabel <file>]
                       (-add <int> | -create <list> | -create-add <list> | -create-seg <list> | -create-seg-mid <int> | -create-viewer <list> | -cubic-to-point | -disc <file> | -project-centerline <file> | -display | -increment | -vert-body <list> | -vert-continuous | -MSE <file> | -remove-reference <file> | -remove-sym <file> | -remove <list> | -keep <list>)
                       [-h] [-msg <str>] [-v <int>] [-qc <folder>]
                       [-qc-dataset <str>] [-qc-subject <str>]

REQUIRED I/O

-i

Input image (Required) Example: t2_labels.nii.gz

OPTIONAL I/O

-o

Output image. Note: Only some label utilities create an output image. Example: t2_labels.nii.gz

Default: “labels.nii.gz”

-ilabel

File that contain labels that you want to correct. It is possible to add new points with this option. Use with -create-viewer. Example: t2_labels_auto.nii.gz

LABEL FUNCTIONS

-add

Add value to all labels. Value can be negative.

-create

Create labels in a new image. List labels as: x1,y1,z1,value1:x2,y2,z2,value2. Example: 12,34,32,1:12,35,33,2

-create-add

Same as -create, but add labels to the input image instead of creating a new image. Example: 12,34,32,1:12,35,33,2

-create-seg

Create labels on a cord segmentation (or centerline) image defined by -i. Each label should be specified using the form v1,v2 where v1 is value of the slice index along the inferior-superior axis, and v2 is the value of the label. Separate each label with :.

Example: -create-seg 5,1:14,2:23,3 adds three labels at the axial slices 5, 14, and 23 (starting from the most inferior slice).

-create-seg-mid

Similar to -create-seg. This option takes a single label value, and will automatically select the mid-point slice in the inferior-superior direction (so there is no need for a slice index).

This is useful for when you have centered the field of view of your data at a specific location. For example, if you already know that the C2-C3 disc is centered in the I-S direction, then you can enter -create-seg-mid 3 for that label. This saves you the trouble of having to manually specify a slice index using -create-seg.

-create-viewer

Manually label from a GUI a list of labels IDs. Provide a comma-separated list containing individual values and/or intervals. Example: -create-viewer 1:4,6,8 will allow you to add labels [1,2,3,4,6,8] using the GUI.

-cubic-to-point

Compute the center-of-mass for each label value.

Default: False

-disc

Project disc labels (-disc) onto a spinal cord segmentation (-i) within the axial plane to create a labeled segmentation.

• Note: Unlike sct_label_vertebrae -discfile, this function does NOT involve cord straightening.

• Note: This method does NOT involve orthogonal projection onto the cord centerline. Details: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/3395#issuecomment-1478435265

The disc labeling follows the convention: https://spinalcordtoolbox.com/user_section/tutorials/vertebral-labeling/labeling-conventions.html

-project-centerline

Project disc labels onto the spinal cord centerline.

-display

Display all labels (i.e. non-zero values).

Default: False

-increment

Takes all non-zero values, sort them along the inverse z direction, and attributes the values 1, 2, 3, etc.

Default: False

-vert-body

From vertebral labeling, create points that are centered at the mid-vertebral levels. Separate desired levels with ,. Example: 3,8

To get all levels, enter 0.

-vert-continuous

Convert discrete vertebral labeling to continuous vertebral labeling.

Default: False

-MSE

Compute Mean Square Error between labels from input and reference image. Specify reference image here.

-remove-reference

Remove labels from input image (-i) that are not in reference image (specified here).

-remove-sym

Remove labels from input image (-i) and reference image (specified here) that don’t match. You must provide two output names separated by ,.

-remove

Remove labels of specific value (specified here) from reference image.

-keep

Keep labels of specific value (specified here) from reference image.

OPTIONAL ARGUMENTS

-msg

Display a message to explain the labeling task. Use with -create-viewer

-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.