Hi Thomas,

Just to add a little to this, note that the case of Siemens mosaics
is where we actually do find the slice timing. Yes, the within-slice
orientation is not really coded well in the DICOM file, but that does
not matter much for most processing. The key is that the location of
the data in space is correct, even if the scanner is reorienting each
slice.

So your slice direction should be correct, and the slice timing should
be read from the DICOM images by Dimon. Note that if you are not using
Dimon but are using to3d directly, use 'FROM_IMAGE' as the slice timing
pattern (meaning to read it from the DICOM files). Try out Dimon
with something like this:

Dimon -infile_pattern '*.dcm' -dicom_org -gert_create_dataset

That should give you an example of how to call to3d directly (in the
resulting GERT_Reco script), on top of creating a dataset.

- rick