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Loading Surfaces

Surfaces can be loaded in Freeview using either the command line or in Freeview. To load surfaces on the command line, use the -f flag.

  freeview -v /path/to/volume -f /path/to/surface

Alternatively, surfaces can be loaded by going to the top menu and selecting File > Load Surface. This will open up a window where you can select the surface you wish to load.

Display Options

The left side panel has a variety of options that can be applied to the loaded surfaces.


These options include changing the color of the surface by selecting a different edge color or changing the thickness of the surface with edge thickness.

Viewing Surface Defects

To view the topological defects and how they were fixed, first run

  defect-seg --s subject

This will take a few min to run. Next, run defect-seg --help to get commands for viewing on the volume or surface. You can replace "tkmedit" and "tksurfer" with "tkmeditfv" and "tksurferfv" to use freeview instead of tkmedit/tksurfer.

To view the defects without using defect-seg, first, load the ?h.orig.nofix surface, then load the ?h.defect_labels as an overlay. Clicking "use surface color" will color the surface regions that have defects, which is very useful for fixing topological errors.

FreeviewGuide/FreeviewWorkingWithData/FreeviewSurfaces (last edited 2017-10-31 16:27:08 by MorganFogarty)