Seeking Free Software to Map P-Values of Brain Regions in Alzheimer's Research

Support & Discussions
1

I am currently conducting research on Alzheimer’s disease and trying to identify the brain regions whose volumes are significantly associated with memory. For each region, I have obtained one p-value that represents the significance for the association. For visualization purpose, I would like to map these p-values to their corresponding regions in a standard brain. I wonder if there is any free software that provides an image of the brain where I can assign each of my p values to its corresponding region in the brain with a color representing the significance. Thank you very much for your help.
Note: The regions I obtained are by segmenting the brain using the software AssemblyNet.

2

This is a very common need in neuroimaging, and fortunately, there are several free tools that can do exactly what you’re looking for.

Since AssemblyNet outputs labeled brain regions (typically NIfTI segmentations), the usual workflow is to assign your p-values to those region labels and visualize them with a colormap on a standard brain. Some good options are:

  • FreeSurfer (FreeView) – If your regions correspond to standard atlases (e.g., Desikan–Killiany / Destrieux), FreeView allows region-wise coloring based on statistical values and produces publication-quality figures.

  • FSLeyes (FSL) – Works very well with labeled atlases and statistical overlays and is fully free.

  • MRIcroGL – Lightweight and easy to use for visualizing volumetric statistical maps and region-wise coloring.

  • BrainNet Viewer (MATLAB) – Popular for clean, region-based visualizations if you’re comfortable with MATLAB.

  • Python (Nilearn) – A great option if you want a reproducible pipeline; you can map p-values to atlas labels and plot them on an MNI brain with custom color scales.

As a side note, since you’re working in Alzheimer’s disease research, you might also be interested in Alzevita, which has recently received**FDA approval for hippocampal volumetric segmentation**. While it’s more focused on clinically validated hippocampal measurements rather than whole-brain visualization, it could be relevant if hippocampal volume is a key region in your study.

Overall, you shouldn’t need any paid software—most groups handle this kind of region-wise p-value visualization using the tools above. The key step is making sure your AssemblyNet regions are aligned to the standard space used by the visualization software.