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Welcome to the ENIGMA-infra guidelines for cortical and subcortical visual inspection!

Quality Assessment: Performing visual inspection

Quality checking is essential to make sure the output that you have produced is accurate and reliable. Even small errors or artifacts in images can lead to big mistakes in analysis and interpretation, so careful checks help us to verify whether we can safely include a certain region of interest or participant in our analysis. For the FreeSurfer output, we will follow standardized ENIGMA instructions on how to decide on the quality of the cortical and subcortical segmentations. At this stage, visual quality assessment of the subsegmentations (e.g., thalamic or hippocampal nuclei) is not required, as there are no established protocols yet and the process would be highly time-consuming; statistical checks (e.g., outlier detection) can be used instead. This may be followed up at a later stage, once there is a project that specifically focuses on these outcomes and the necessary anatomical expertise is available to develop a dedicated quality control manual.

Important notes for viewing and copying files

Locally

  • We strongly recommend downloading the entire output folder locally before opening the HTML file. Opening the HTML on a server or network drive is often slow and may cause images not to load properly.
  • When copying files, make sure to include all generated folders (such as screenshots, surfaces, etc.) along with the fsqc-results.html file. These folders contain the images referenced in the HTML and are essential for proper display.

On the server

  • If you have not experienced such issues before and prefer to work directly on your server, you can instead open the HTML file in your available browser (for example: firefox fsqc-results.html).

Final check

  • When opening the fsqc-results.html file:
  • Scroll through the subjects to confirm all images load and no data is missing.
  • Click on any image to zoom in, or right-click and choose “Open in new tab” and inspect details more closely.

You can find the updated ENIGMA-PD QC instructions for visual inspection here.