Nov 14, 2023
Visualign Transformation
- Michael X. Henderson1
- 1Van Andel Institute
- Michael X. Henderson: ORCHID: 0000-0001-9710-0726
Protocol Citation: Michael X. Henderson 2023. Visualign Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.5qpvo38odv4o/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 16, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 90664
Keywords: ASAPCRN
Funders Acknowledgement:
National Institute on Aging
Grant ID: R01-AG077573
Aligning Science Across Parkinson’s
Grant ID: ASAP-020616
Abstract
This protocol describes visualign transformation.
Attachments
812-2118.pdf
4.6MB
Visualign Transformation
Visualign Transformation
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 location.
Crosses can be moved at any point. They can also be deleted by hovering over them and clicking Delete on the keyboard.
Note
Tip: start with outer alignments before moving onto inner.
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.