Inner Cortical Surface


This module generates a surface mesh based on the cleaned and corrected inner cortical boundary mask.

If adjusting the parameters of this stage does not produce a satisfactory surface, rerun the stages that created the mask (cortex mask selection, scrub mask, topology correction, and wisp removal) and change the parameters to achieve a better foundation mask with which to generate the surface.


Smoothing iterations (typical range is 5–20)
Number of smoothing iterations to apply.
Smoothing constant (typical range is 0.1–1)
The strength of the smoothing, ranging from 0 (no smoothing) to 1 (most smoothing).
Curvature weight (typical range is 1–5)
Adjusts the smoothing based on a measure of local curvature

Command-Line Usage

dfs: generates mesh surfaces using an isosurface algorithm.

usage: dfs -i input -o output [optional settings]

example: dfs -i input_mri.nii.gz -o surface.dfs

Required Settings:
Flags Description
-i <input volume> input 3D volume
-o <output surface> output surface mesh file
Optional Settings:
Flags Description
-c <image volume> shade surface model with data from image volume; a set of vertex colors is generated within the file
-n <value> number of smoothing iterations [default: 10]
-a <value> smoothing constant [default: 0.5]
-w <value> curvature weighting [default: 0]
-f <value> scaling percentile [default: 0.999]
-nz tessellate non-zero voxels
-gt <threshold> tessellate voxels greater than <threshold>
-lt <threshold> tessellate voxels less than <threshold>
-eq <value> tessellate voxels equal to <value>
-z zero-pad volume (avoids clipping at edges)
--nonormals do not compute vertex normals
--postsmooth smooth vertices after coloring
-v <level> verbosity (0 = quiet) [default: 1]
--timer timing function

Example Result


If “save output of each stage automatically” is checked on the Cortical Surface Extraction sequence, the following files are generated (where filename_prefix is the filename of the MRI scan without the file extension, e.g. “testsubj” for the file “testsubj.nii”):

Filename Contents
filename_prefix.inner.cortex.dfs Surface representing the boundary between white matter and cortical grey matter. Provides the foundation for the generation of the pial surface in the next step.

Restore from Previous Session

If BrainSuite was interrupted while performing this stage or to change the parameters for this stage and rerun after fully processing a scan, click “Restore From Previous…” on the bottom of this stage’s dialog box and load the original MRI scan. BrainSuite will automatically load all of the files generated in previous stages, allowing processing to restart from this intermediate stage.