Some Slicer caveats and some possible solutions

Slicer is a research effort and a work in progress. As such, there are many features that don't always work in all cases. Here are some known issues and some ways to deal with them.

• My data is 512x512 resolution and this seems to confuse Slicer.

  Originally, Slicer was designed for images that are 256x256 resolution. However, Slicer has been modified to accommodate 512x512 and larger images. If your data is 512x512, and Slicer is still having difficulties handling it, try reducing the resolution of your data to 256x256 resolution. If you do this, please realize that:

  • Your reduced number of pixels will now be twice as big as they were, since there are half as many pixels in the X direction and half as many in the Y-direction after reduction.
  • In most cases, the reduced data sets look visually acceptable. But, since there is one-fourth the information in each reduced slice, some smaller structures may not be acceptable for viewing or editing.

• The headers on my data are confusing Slicer.

  Some users find that things work best if they record the information about their images manually, and then throw the headers away. Any data that you create and save with Slicer will be written out in no-header format and numbered slice.001 to slice.xxx where xxx is the highest numbered slice.

• When I try to save my changes, Slicer crashes and prints a "Segmentation fault" message.

  Segmentation fault is usually caused by one of two reasons:

  • The user is trying to write data to a directory that is owned by another user.
  • The user is trying to write data to a full file system. To check if the file system is full, change to the directory where the data is and try to copy one image to a temporary file in the same directory (for example, cp I.001 junk). If this does not work, then the file system is likely full. Note that the df command does not always give the correct results, so the above approach is preferred