New neuromaps annotation

natepetro · October 7, 2025, 4:51pm

Greetings,

I am hoping to use the Sydnor SA-axis annotation that is included in the neuromaps toolbox. Is it possible for this to be added to the available annotations in the neuromaps plugin? Or, is it possible to take the Sydnor annotation that I obtained using neuromaps (as fsLR 64k gii file) and import into my brainstorm protocol?

Thank you for your time.

Raymundo.Cassani · October 8, 2025, 5:21pm

Hello @natepetro,

Yes this map can be added in the plug in. I'll let you know when it is ready.

It is not possible to use the 64k .gii file directly in Brainstorm. This is because the downsampled FSAverage cortices are not the same in neuromaps and in Brainstorm.

What is possible is to import the 164k .gii files, in Brainstorm to a Subject using the FSAverage template (as the high resolution cortices are the same in neuromaps and Brainstorm). From there, you would need to project the map to the DefaultAnatomy ICBM152. This is in fact how the available maps in the plugin are processed:

github.com/thuy-n/bst-neuromaps

generate_bst_plugin_maps.m

main

function generate_bst_plugin_maps()
% GENERATE_BST_PLUGIN_MAPS
%
% USAGE: generate_bst_plugin_maps(bstNeuromapsDir)
%

% 'bst-neuromaps' and 'brainstorm3' are expected at the same level
bstNeuromapsDir = bst_fullfile(fileparts(bst_get('BrainstormHomeDir')), 'bst-neuromaps');
if ~exist(bstNeuromapsDir, 'dir')
    return
end

% Annotations fetched from neuromaps
% Surface: FsAverage space with 327,684 vertices (~164k vertices per hemisphere)
% Volume:  MNI152 space 1mm [193x229x193]
nmpSurfMapsDir = bst_fullfile(bstNeuromapsDir, 'tmp', 'surface');
nmpVolMapsDir  = bst_fullfile(bstNeuromapsDir, 'tmp', 'volume');

% Annotations are imported in Brainstorm MNI ICBM152 default anatomy
% https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy

This file has been truncated. show original

EDIT: I just realized fsLR and fsaverage surface-based coordinate systems are note the same, even for 164k vertices

Raymundo.Cassani · October 9, 2025, 8:56pm

@natepetro, the sydnor2021-SAaxis is now in the bst-neuromaps plugin!

In Brainstorm, go to Plugins > Anatomy > neuromaps > Update

natepetro · October 28, 2025, 5:20pm

Hey Raymundo,

Thanks so much for getting to this so quickly. I had to put this project on hold for a few days, so I apologize for the slow response.

I noticed the SA annotation didn’t line up with what I expected to see. I looked at some of the other neuromaps annotations, and it appears that the SA annotation is a duplicate of the GABAa/bz_flumazenil_dukart2018_N6_Age43 annotation.

when I view the SA annotation that I retrieved from NeuroMaps, it looks like this (with values from about -1.98 - +1.98).

Sorry for the bother and let me know if this is something that can be fixed. Thanks for all your help!!

Raymundo.Cassani · October 29, 2025, 1:55pm

Hi Nate, there was indeed a typo on the code on transforming from the fsLR space, so the last converted map (which was GABAa/bz_flumazenil_dukart2018_N6_Age43) was retrieved.

It is now fixed, please update the plugin and fetch the SAxis map

natepetro · October 29, 2025, 2:44pm

Looks great! Thanks so much for the quick turnaround!