'Check if DISPLAY variable is set' fail in sct_check_dependencies

Hello,

I am using a macOS and I just completed the installation process for the lastest version (4.3). I ran sct_check_dependencies and that was the only one that failed. Would you be able to help me how I could troubleshoot this? In addition, I just realized that the testing for ‘Check if figure can be opened with PyQt’ did not run. How would I check for that as well? Thank you.

Hi,
Could you please copy/paste the output of you Terminal?
Thanks

Spinal Cord Toolbox (4.3)

SCT info:

  • version: 4.3

  • path: /Users/kim/sct_4.3

OS: osx (Darwin-19.6.0-x86_64-i386-64bit)

CPU cores: Available: 8, Used by SCT: 8

RAM: Primary memory available: 8.00 gigabytes

Check Python executable…[OK]

Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 17:50:39)

[GCC Clang 10.0.0 ] at /Users/yujinkim/sct_4.3/python/envs/venv_sct/bin/python

Check if data are installed…[OK]

Check if numpy is installed…[OK] (1.18.5)

Check if colored is installed…[OK] (1.4.2)

Check if dipy is installed…[OK] (1.1.1)

Check if futures is installed…[OK]

Check if h5py is installed…[OK] (2.10.0)

Check if ivadomed (1.2.1) is installed…[OK] (1.2.1)

Check if Keras (2.1.5) is installed…[OK] (2.1.5)

Check if matplotlib is installed…[OK] (3.2.1)

Check if nibabel is installed…[OK] (3.1.0)

Check if pandas is installed…[OK] (1.0.4)

Check if pyqt5 (5.11.3) is installed…[OK] (5.11.3)

Check if pytest is installed…[OK] (5.4.3)

Check if pytest-cov is installed…[OK] (2.9.0)

Check if raven is installed…[OK]

Check if requests is installed…[OK] (2.23.0)

Check if requirements-parser is installed…[OK] (0.2.0)

Check if scipy is installed…[OK] (1.4.1)

Check if scikit-image is installed…[OK] (0.17.2)

Check if scikit-learn is installed…[OK] (0.23.1)

Check if tensorflow (1.5.0) is installed…[OK] (1.5.0)

Check if torch (1.5.0) is installed…[OK] (1.5.0)

Check if torchvision (0.6.0) is installed…[OK] (0.6.0)

Check if xlwt is installed…[OK] (1.3.0)

Check if tqdm is installed…[OK] (4.46.1)

Check if transforms3d is installed…[OK] (0.3.1)

Check if urllib3 is installed…[OK] (1.25.9)

Check if spinalcordtoolbox is installed…[OK]

Check ANTs compatibility with OS …[OK]

Check PropSeg compatibility with OS …[OK]

Check if DISPLAY variable is set…[FAIL]

Would it be perhaps because I need to install another viewer program (I don’t know the exact terminology, my apologies), such as FSL/FSLeyes software?

no, that is not a requirement. We are aware of this issue (see here). Are you able to properly run sct_label_utils -i IMAGE -create-viewer 3? (ie: does a window pop up)?

This is what I got:
Spinal Cord Toolbox (4.3)

DESCRIPTION
Utility function for label image.

USAGE
sct_label_utils -i

MANDATORY ARGUMENTS
-i Input image.

OPTIONAL ARGUMENTS
-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, …
-create-add Same as “-create”, but add labels to the input image instead of
creating a new image.
-create-seg Create labels along cord segmentation (or centerline) defined by
“-i”. First value is “z”, second is the value of the label. Separate
labels with “:”. Example: 5,1:14,2:23,3. To select the mid-point in
the superior-inferior direction, set z to “-1”. For example if you
know that C2-C3 disc is centered in the S-I direction, then enter:
-1,3
-create-viewer Manually label from a GUI a list of labels IDs, separated with “,”.
Example: 2,3,4,5
-ilabel File that contain labels that you want to correct. It is possible to
add new points with this option. Use with -create-viewer
-cubic-to-point Compute the center-of-mass for each label value.
-display Display all labels (i.e. non-zero values).
-increment Takes all non-zero values, sort them along the inverse z direction,
and attributes the values 1, 2, 3, etc.
-vert-body From vertebral labeling, create points that are centered at the
mid-vertebral levels. Separate desired levels with “,”. To get all
levels, enter “0”.
-vert-continuous Convert discrete vertebral labeling to continuous vertebral labeling.
-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
MISC
-msg Display a message to explain the labeling task. Use with
-create-viewer.
-o Output image(s). Default value = labels.nii.gz
-v {0,1,2} Verbose. 0: nothing. 1: basic. 2: extended. Default value = 1

Command-line usage error: Option -i file doesn’t exist: IMAGE
Aborted…

“IMAGE” was just an example, you need to try with an actual nifti file