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MRIcroGL includes basic drawing tools that allow you to mark regions of interest such as the extent of brain injury or an anatomical area such as the hippocampus. These regions of interest can be used for statistical analysis, for example conducting conducting region of interest analysis for fMRI studies, generating peristimulus plots, and conduction lesion symptom mapping. The basics are shown in this YouTube video (which includes text annotations if your browser supports them). 

Getting Started

Here are basic instructions for drawing a region of interest with MRIcroGL.

  • Launch MRIcroGL and open the MRI you want to draw on top of by selecting File/Open.
  • (optional) If you want to edit a previously created drawing you can open it with Draw/Open, otherwise go directly to the next step to create a new region.
  • Use the Display menu to select the 2D view you want to draw on. For example choose the Display/Axial view if you want to draw your region on transverse slices. You can draw on any of the 2D slices (axial, coronal, sagittal or multi-planar) but not on the 3D rendering.
  • Select Draw/DrawColor to select the pen tool. For example, choose Draw/DrawColor/Red to select the red pen.
  • Drag the mouse around the outline of you region. The software will automatically fill in the region
  • You can shift-drag to erase regions.
  • You can option-click to fill regions (see the Flood Fill section), and shift-option-click to erase contiguous regions.
  • If you make a mistake, use Draw/Undo.
  • To change the displayed slice use the left and right arrows (to move left and right), the up and down arrows (to move superior and inferior) and the home/end keys (to move anterior and posterior, for OSX these are the Fn+LeftArrow and Fn+RightArrow keys).
  • Note you can use the Draw/Transparency menu items to adjust the contrast of your drawing or to briefly hide the drawing to better see the contours.
  • When you are done drawing, you can choose Draw/Save to save your region.
  • Once you are finished, you can choose Draw/DrawColor/None to turn off the drawing mode This allows you to click on the slices to change your view.

Flood Fills

When you are drawing, you can option-click a location to make all the contiguous voxels connected to the clicked location have the active color. For example, if you have the red pen selected, clicking an unmarked (clear) region will fill all contiguous voxels red. If you shift+option+click a location you will erase all the contiguous voxels, so shift-option-clicking a red location will erase all the connected red voxels. The fill works a little different if you click a location with the selected color, in this case you will generate a bubble fill, so option-clicking a red voxel with the red pen will select all the contiguous red voxels and fill any bubbles in this object with red. These options are illustrated in the image. The top row shows the initial image. The bottom row shows the effect of a fill or erase applied to the location of the crosshair.

Smooth and Refine

When we draw pixels with a mouse, our hand often shakes a little leading to slightly jagged edges. In addition, we typically draw in one slice orientation (e.g. on axial slices) and typically emphasize edges observed within these slices rather than between slices. Therefore, slices look a bit jagged when we view them from a different orientation (e.g. on coronal slices). In general, these are probably small inconsistencies that have little meaningful influence on our analysis. However, MRIcroGL has a special function (Draw/Advanced/SmoothAndRefineDrawing) that attempts to refine your drawing a little bit. You should use this after you have completed your drawing. It attempts to balance a few factors: smoothing the image in 3D space (to minimize sharp edges dues to noise), to make all the voxels in the drawn region have similar colors (e.g. if you drew a lesion that appears bright, than edge voxels that are dark will be removed) and trying to maintain the overall volume of your drawing. If you do not like the results of this refinement you can choose Draw/Undo to revert back to your original drawing.

Advanced Drawing

Note that by default you can select from 9 distinct draw colors to mark different mutually exclusive regions. When creating a drawing with multiple colors, you may want to toggle the Draw/Advanced?overwriteDrawColors option – this determines whether your selected pen paints all voxels or only the voxels that have not been previously colored. The Draw/Advanced/CustomDrawColors allows you to import a ITK-SNAP labeling file that can specify the color and name for up to 255 distinct regions. MRIcroGL is very simple when you want to mark a few colors, but for complex jobs you may find ITK-SNAP a better tool.


  • ITK-SNAP is useful for challenging drawing tasks. The drawing tools are a bit different, but since it also supports NIfTI format images you can choose the best tool for your specific project (or even use MRIcroGL and ITK-SNAP to refine a drawing).
  • Slicer includes drawing tools.
  • AFNI also includes tools for defining regions of interest. 
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