Amira workflow

DICOM processing

When loading directories of dicoms into Amira, it seems to get get confused for two reasons.

1. CT scans were performed in stages, and
2. these stages overlap, causing fragmentation and repetition of data.

Consolidation

consolidate.m attempts to overcome this by looping through directories, checking each .dcm file's SliceLocation, and copying the .dcm files to a new directory whose SliceLocation had not been checked.

The hope is, with this, Amira will be able to import this new directory as a single dicom stack with which to generate surface and volume information.

Unresolved Question: Is this code general enough to handle all stacks of dicoms? Should this code be expanded to handle other file formats?

Known Problems: Windows style filepaths cause consolidate.m to throw errors when attempting to copy files to a new directory on a non-Windows macine. Changes can be made to be made to automatically adopt the system's filepath convention.