Open Visualign program from folder on the desktop.

File > Open > select “ QuickN JSON ” you created in QuickNII.

Drag the opacity bar all the way to the right to where it says outline, and you will have all outlined regions displayed. This is the easiest format for transformation.

Align all regions properly.

Hover over an atlas region.

Click the SPACE bar .

Drag the cross symbol to the correct .

Crosses can be moved at any point. They can also be deleted by hovering over them and clicking Delete on the keyboard.

Click the < and > arrows at the top right to navigate between sections. There is no need to “Store” these as in QuickNII. See a finished section below.

Once completed, click File > Save As > save “ Visualign JSON ” in the QVN folder. This can be opened again to continue aligning later.

To convert into a flat file, click File > Export , navigate to the Atlas folder and click “Select Folder”. This will export the files needed for Nutil .