Rick,

Quick update and questions:

I looked into which files dimon was missing when using the -dicom_org option. It turns out it was excluding the first volume and the last two volumes of the run. I'm still not sure why; I don't see anything special about those particular DICOM files.

I also tried running dimon without -dicom_org and it seemed to correctly identify the number of slices per volume and the number of volumes. It also "found" all of the images in the directory. The call to to3d it produced successfully created an AFNI BRIK with the expected number of volumes and slices.

I have some questions/concerns about using dimon without the -dicom_org option, however.

Does dimon do any sort of file order checking without the -dicom_org option, or would the files need to be in the correct order in the directory prior to dimon being used? If the latter, what order does dimon assume the files are in?
It seems to like them grouped by volume and then by slice position (rather than all the time points for the first slice followed by all the time points for the second slice, etc.).
If the data I'm dealing with are sagittal slices, how do I order the files such that dimon puts the files together correctly in terms of left/right (does it want the left side of the brain fed in first or the right side first, or does it depend on the order in which the slices were acquired)?

Thanks,
-John