Current processing structure
Below is a summary of current processing streams for data from trailer (um-stream8) and inside (um-flex, pre_beta release) scanners.
New processing structure (um-flex)
um-flex (1.0b) is more flexible than previous stream versions. Specific processing modules can be selected and the order in which they run can be configured.
Note that the output of all these steps is in NIFTI format. In a nutshell, the whole time series are stored in a single file sequentially and a header is pre-pended to the file. The images names end in .nii. Here is a matlab program to convert from NIFTI to 4D Analyze format.
Below is an example of the new directory structure: