Inspecting the results of your analysis (Quality Control, FSLeyes)#

Quality Control (QC) Reports#

SCT provides a web browser-based interface called a Quality Control (QC) Report. Each QC report contains a table of image entries. Clicking on an entry in the table will show a mosaic of slice images, as well as an overlay that can highlight cord segmentations, WM/GM tract volumes, and more.

How can I generate a QC report?#

To generate a QC report, check to see if the command you’re using supports the -qc flag. For example:

# Basic command (no QC)
sct_propseg -i t2.nii.gz -c t2

# Command with QC flag added
sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_folder

Once you specify the -qc flag, a QC report will be automatically generated in whichever folder you specified. You can specify the same folder as many times as you like.

How do I open the QC report?#

At the very bottom of the terminal output for your command, instructions will be printed to help you open the QC report:

# Sample output (macOS) after running the SCT script
Use the following command to see the results in a browser:
open "qc_folder/index.html"
# Sample output (Linux) after running the SCT script
Use the following command to see the results in a browser:
xdg-open "qc_folder/index.html"

If you already have the page open, and you run new commands, you can simply refresh the page to display new QC report entries.

How do I use the QC report?#

Once you run the open command, the QC report page will open up in your web browser for you to interact with.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/quality-control/qc.png

From the table on the left side, you can:

  • Navigate between images using the arrow keys or mouse.

  • Toggle the overlay using the right arrow key.

  • Evaluate and mark images using the f key. Pressing once marks the highlighted image as “Pass”, twice marks it as “Fail”, and three times marks it as “Artifact”.

  • Export the marked images in a list format using the buttons at the bottom of the table.

This workflow is especially useful if you are performing multi-subject batch analyses, as QC reports allow you to quickly review many output files at once using your keyboard.

FSLeyes#

If you have the FSLeyes tool installed, then some of SCT’s scripts will also print a fsleyes command as part of their output.

# Sample output after running an SCT script
Done! To view results, type:
fsleyes t2/t2.nii.gz -cm greyscale t2/t2_seg.nii.gz -cm red -a 100.0 &

Running this command will display a viewer that you can interact with. For more information about how to use FSLeyes, visit the FSLeyes documentation.

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/quality-control/fsleyes.png