Up to FreeviewGuide

Back to FreeviewManualTransformation

Continue to FreeviewDTI

Surfaces

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.

Surfs_panel.png

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)