Sorry for the delay. This was quite a bit more complicated than we had hoped. Rick Reynolds and I have spent some time on this problem. This Siemens DICOM data is both oblique and in reversed order in the mosaic EPI data and in the non-mosaic anatomical data. Changes that will be available in the next binary distribution will allow you to read the data in like this. The option -oblique_origin has been added to to3d and to 3drefit to reset the origin and orientation from the obliquity transformation matrix. Another option, -reverse_list, makes it more convenient to reverse the order of the list.

# for the anat dataset, reverse the list of files
to3d -prefix anat -reverse_list 2dAnatomy/*.dcm

# for the epi dataset, use origin computed by obliquity
# epi dicom data is in current directory and in mosaic format
to3d -prefix epi -oblique_origin *.dcm

If you didn't use the -oblique_origin option, the origin could later be applied with the new option of the same name for 3drefit:

3drefit -oblique_origin epi+orig


Alternatively, datasets can always be read in more generically specifying the fields of view and orientation like this.

# (right to left, then superior to inferior and then slices posterior to inferior)
to3d -prefix anat96_24 -xFOV 96R-L -yFOV 96S-I -zFOV 24P-A 2dAnatomy/*.dcm
# for the EPI, the data appears to be RSA (slices are in opposite order-reversed by a scanner
# display setting)
to3d -prefix epi96 -xFOV 96R-L -yFOV 96S-I -zFOV 24A-P *.dcm

# remove the obliquity information from the datasets because it's not right anyway
3drefit -deoblique anat96_24+orig
3drefit -deoblique epi96_24+orig