Hello,

I'm a first-time SLOMOCO user attempting basic usage on a single epi run. I am running into difficulty that I believe originates in a slice acquisition timing error (in bold below; ERROR: all slice acquisition timing was time-shifted to zero). This error seems to result in a failure to write the dataset epi.r01.slicemocoxy_afni+orig to disk.

I also receive several warnings about oblique data, but it is my understanding these are not of concern here.

slicemoco_newalgorithm.sh -d epi.r01

...
++ Max displacement in automask = 0.79 (mm) at sub-brick 191
++ Max delta displ in automask = 0.61 (mm) at sub-brick 79
++ Wrote dataset to disk in ./epi.r01.mocoafni.hdr
/Users/lrweiss/pestica4/slomoco/run_correction_slicemocoxy_afni.sh -b epi.r01 -p epi.r01.slicemocoxy_afni
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./epi.r01+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./epi.r01+orig.BRIK is 29.155983 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./epi.r01+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./epi.r01+orig.BRIK is 29.155983 degrees from plumb.
using "-parfix 3 0 -parfix 5 0 -parfix 6 0 -parfix 9 1 -parfix 11 0 -parfix 12 0" to fix to in-plane motion
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./epi.r01+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./epi.r01+orig.BRIK is 29.155983 degrees from plumb.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./epi.r01+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./epi.r01+orig.BRIK is 29.155983 degrees from plumb.
doing 36 slices with 246 timepoints
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./epi.r01+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./epi.r01+orig.BRIK is 29.155983 degrees from plumb.
ERROR: all slice acquisition timing was time-shifted to zero
/Users/lrweiss/pestica4/slomoco/run_slicemoco_inside_fixed_vol.sh -b epi.r01.slicemocoxy_afni
*** Can't open dataset epi.r01.slicemocoxy_afni+orig
doing slices with -1 timepoints
*** Can't open dataset epi.r01.slicemocoxy_afni+orig
ERROR: slice acquisition timing does not have zero

Any input on the cause of this error? This epi dataset is from a Siemens scanner with ascending interleaved acquisition.

Many thanks

-Lauren

If this is helpful to anyone in the future:

I dug back and discovered the .dcm images were originally reconstructed using Dimon and the -from_image flag on the to3d command.

When I went back and reconstructed without this option, the script worked.