Computer Vision News - March 2020

3 Summary FSL Mask Extraction 19 The GUI is very intuitive . We can change opacity, brightness and contrast from the slides on top, we can also select different modes for the visualization, zoom in and zoom out and move through the 3D coordinate space by just moving over the cursor following the directions (S-superior, I-inferior, P-posterior, A-anterior, R-right, L-left). We can also modify the range of the image using min and max value on top and see what happens if we apply thresholds to the image. Finally, we can load other files which will appear in the overlay list and then either decide to show only some by clicking on the eye icon or changing colour scale in order to visualise differences/similarities between images and overlapping. In Figure 3, the structural brain mask is overlaid on top of the structural MRI image showing the result provided by the bet tool used before. If we now want to visualise the main output, we just need to turn off the two layers, and activate the structural_brain one. This should be displayed as below. Similar to the application just covered, FSL can also help select specific Regions of Interest (ROIs) by loading pre-made atlases or based on contrast threshold. Moreover, FSLeyes offers the opportunity to define a self-made ROI using drawing tools. FSL is a multi-use software tool which can fit several imaging tasks. The GUI style results intuitive enough to be used without any particular programming knowledge. Nonetheless, experience with linux command line might help speed up the process and result in a faster and easier way to use the different tools. We started by showing one of the many applications of FSL, but we are keen to explore multiple other ones (e.g. integration with MatLab/Jupyter notebooks) in future articles. Conclusion Figure 3