Neuroimaging Visualization Resources - GarzaLab/Documentation GitHub Wiki
Visualization resources!
A list of resources compiled during the OHBM Brainhack 2020.
Additional Visualization Tools findable here via NITRC.
| Tool | Pros | Cons | Examples |
|---|---|---|---|
| MIPAV | Very versatile 2D/3D/4D viewer, with lots of tools for trying out simple image analysis. Great set of tools for manual delineation. Very nice volumetric and surface 3D rendering engine. | Tends to mess up Nifti headers when writing images, can be overwhelming. | Tends to mess up Nifti headers when writing images, can be overwhelming. |
| pysurfer | You are limited to freesurfer generated surfaces and annotations | ||
| mrivis | Carpet plots and advanced classes for slicing and dicing n-dim images (3D/4D/nD); various methods of comparing alignment | No CLI | https://raamana.github.io/mrivis/vis_classes_usage.html |
| Mango | User-friendly GUI, surface and slice options, configurable layouts, includes template and colormap creation options | GUI-based, less well-suited for automation | Download + info, surface + slices example |
| CARET | |||
| Brain Life | Integrated platform, pretty, can import data via datalad | a singular instance in the world | |
| Nilearn | Tools for surface, activation, connectome, ROIs, etc. etc., pythonic! , easy to use, well-documented, lots of available examples, built-in template and atlas fetching, can automate figure curation | python (a con if you're not a python user) | Nilearn reference |
| bioimagesuite | Web UI, datasets.datalad.org support | Web UI | |
| Plotly | Text | Text | |
| fsleyes | versatile | ||
| AFNI, SUMA | mature, VERY versatile | old, works best with BRIK/HEAD | |
| MRIcroGL | pretty pictures, scriptable, Really fast and easy way to view volumes in 3-D, no freesurfer needed. | Can be a little fiddly, need to make a nifti for each element you want to visualize. | Figure 1B here and 1A here are some of the better ones I've made. |
| Gephi | create graphs | not trivial to install | |
| BrainSpace | Available in both Python and MATLAB. Looks good out-of-the-box. | Currently lacks simple figure customization. | |
| BrainNet | |||
| Display | Part of the MINC-toolkit. Maintains orientations and easy to use. MINC or NIFTI | Steep curve to learn | |
| register | Part of the MINC-toolkit. Compares any type of image side to side, maintaining orientations. | No tutorials |
Some guidelines, tools, and helpful tutorials
| Source | Description |
|---|---|
| Visualization Cheat Sheets | |
| Paletton | Great complementary color picker, good for making discrete color maps |
| Data to Viz | |
| Fundamentals of Data Visualization | Free e-book on data visualization |
| Gallery of D3 visualizations | Nice source of inspiration (cf DataViz) |
| Visual Vocabulary | Another chart/graph picker site. |
| Guidelines on color-blindness figures | |
| Colorcet | Categorical colors |