This tool allows loading your CSV table and explore it with your web browser. It is useful in one-by-one qc analysis by scrolling line by line and rating using dropdown menu. Results can be saved as the new CSV table.

Find table viewer in lobi-mri-scripts repo

Run with: python -m http.server --cgi and go to localhost:8000

Hints:

• Utilize the save button to persist your changes. Changes will be not saved automatically!
• Input your own command into a text field for execution on each table row, for example: freeview -v $SUBJECTS_DIR/$subj/mri/T1w.mgz. Use $subj to be replaced by the respective labels.
• Rows labeled "low" and "high" serve to define lower and upper thresholds. Values outside these limits will be colored yellow.
• Images named the same as the index column ({subj}.svg) will be loaded automatically from the ./imgs if exist. You can change image type to be displayed in the first line of script.css (default SVG)
• Adjust image size by modyfing CSS fields in index.html - left, bottom and width (zoom)

Example for group_bold.tsv (mriqc for BOLD images):

1. Check what columns are available and their indices awk -F'\\t' 'NR==1 {for(i=1; i<=NF; i++) print i". " $i}' group_bold.tsv
2. Export those columns to a new CSV file cut -f 1,12,20,45 group_bold.tsv | tr '\\t' ',' > data.csv
3. (Optionally) Add lower and upper bounds for cell colouring. Manually add two lines (copy and modify existing ones), rename them to 'low' and 'high' and modify respective values.
4. Run python server python -m http.server --cgi and go to localhost:8000
5. (Optionally) Run the second http server in mriqc directory to display full featured mriqc reports with python -m http.server 8001 and Run command as following open localhost:8001/$subj.html
6. (Optionally) Add some thumbnail images by copying them from mriqc find ./mriqc -iname *desc-zoomed_bold.svg -exec cp {} ./table-viewer/imgs \\; , rename them (remove desc-zoomed) to match subjects’ ids and adjust visibility.