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
Hello,
I am still stuck on this issue which may be causing the software/viewer not detect the spinal cord as red. My sct_check_dependencies still show ‘Check if DISPLAY variable is set… [FAIL]’ but everything else works. The viewer that I am utilizing- FSLeyes is not detecting the spinal cord area as red. Would you be able to help me solve this issue? Before updating my Mac to Big Sur, it has been working, but now it does not.
Hello kim,
The Check if DISPLAY variable is set… [FAIL] is not the source of your problem. It is a check that can sometimes fail in some environments (in fact it is a bad check, we will probably remove it).
Can you explain in more details what precisely your issue is and include the following:
Regards,
I am tagging the issue as “resolved” as there is no news from the user after 1 month.