Plotting MRI figures from SPM

andreacopu · April 17, 2024, 4:23pm

Hi neuroimagers!

I am trying to create nice figures for a paper i am writing about associations between fitness and gray matter volume using a whole brain analytical approach. I used SPM for this vbm analyses.

My question is: does anyone know how can i extract each cluster individually from the results.nii file in a independent .nii file using mricrogl, or fsleyes or itk-snap?

Thank you so much!!

Remi-Gau · April 18, 2024, 8:03am

If you have access to SPM with octave or SPM I had put aside some functions to help do things like this.

Some of the code was taken from there: SPM/How-to - Wikibooks, open books for an open world?

github.com

cpp-lln-lab/CPP_ROI/blob/main/demos/roi/label_and_extract_clusters.m

% (C) Copyright 2021 CPP ROI developers

%
% scripts to transform a probability map from neurosynth
% into an image with fewer clusters (apply peak and extend threshold) and
% where each cluster has one label.
%

run ../../initCppRoi;

gunzip(fullfile('inputs', '*.gz'));

zMap = fullfile(pwd, 'inputs', 'visual motion_association-test_z_FDR_0.01.nii');
zMap = renameNeuroSynth(zMap);

peakThreshold = 5;
extendThreshold = 50;

zMap = renameNeuroSynth(zMap);

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