[MINC-users] Time frame start values

[Robert D. Vincent]

Hi Alex,

I've heard of these issues in a number of instances, I am (slowly, when
time permits) trying to resolve one particular case in dcm2mnc.

PET files often use the DICOM field 0054:1300, the "Frame Reference Time",
as the main (or only) indication of PET frame start times. However, as you
can see at the link I have provided, the exact meaning of this field is
undefined, so it is unusually worthless even for DICOM. Some PET sequences
use other fields to indicate the frame times, but consistency here is poor.

https://www.dabsoft.ch/dicom/3/C.8.9.4.1.5/

My intended solution is to use the frame widths ("Actual Frame Duration",
0018:1242) to reconstruct the MINC dimension by simply setting the start
time of each frame to the sum of the preceding frame widths. This relies on
the accuracy of these frame widths, but in my experience this may be more
reliable than relying on the frame times. However, if the frame times are
somehow meaningful, that information will be lost (or at least not stored
in a standard place). So my plan is to make this depend on a command line
option.

    -bert

On Thu, Mar 28, 2019 at 9:15 AM Alex Zijdenbos <zijdenbos at gmail.com> wrote:

> Hello all,
>
> I've running into an issue I don't know what to do with (yet). How are (or
> should) start values be interpreted in a MINC time-dimension?
>
> For spatial dimensions, the voxel positions are in the center of the voxel;
> but in converting dynamic PET data from various scanners, we are seeing
> what looks like variations between scanners in terms of whether the start
> is center-frame, or start-of-frame.
>
> We also sometimes end up with negative time steps out of dcm2mnc, which
> calls into question whether (a) that should ever happen; and (b) how for
> example mincreshape behaves when re-ordering that dimension. My assumption
> is that mincreshape will interpret the start to be center-frame, and that
> therefore changing the sign of the time-step might end up with a wrong
> start value.
>
> If anybody has thoughts about or experience with these issues, please share
> :-)
>
> Thanks,
>
> -- A
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