open-discussion > Brain coordinates to AAL regions
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May 11, 2023  10:05 AM | tammartru
Brain coordinates to AAL regions
Dear Dr. Rorden,

I am writing to inquire if there is a method to input a list of brain coordinates into MRIcroGL and obtain the corresponding regions based on the AAL atlas, similar to the functionality available in the xjview software.

Thank you very much for your assistance.

May 12, 2023  12:05 PM | Chris Rorden
RE: Brain coordinates to AAL regions
I would suggest writing a JavaScript script for NiiVue to solve this.

You can interactively see how using the mouse to different locations updates the text show in the bottom core. The documentation describes a function moveCrosshairInVox() that could automate this:
May 15, 2023  11:05 AM | tammartru
RE: Brain coordinates to AAL regions
Dear Dr. Roden,

Thank you for your suggestion and prompt responses.
I have a couple of questions regarding the usage of JavaScript in the script window of MRIcroGL. Can JavaScript be used in the script window, and do I need to import the niivue library to my computer for that purpose?
I also noticed that the coordinates in the featured atlas are represented by numbers instead of labels. Is there a step I'm missing to convert these numbers to anatomical AAL labels?

I understand that this may go beyond the capabilities of MRIcroGL, but I appreciate your assistance nonetheless.

Thank you for your ongoing support!
May 15, 2023  12:05 PM | Chris Rorden
RE: Brain coordinates to AAL regions
MRIcroGL is a native executable that uses Python for scripting. NiiVue is built from JavaScript, and is therefore inherently scriptable. You can put script calls directly into your web pages, or have users enter scripts in edit boxes. Here is an example of the latter approach: