[MINC-users] dcm2mnc for Siemens Biograph mCT 64 PET/CT scanner

[Yoshitaka KUMAKURA]

Thank you very much, Andrew and Vladimir.

Here is my progress.

1)    I've installed dcm2mnc version 2.01.01 (built  2015), and found it
working much better. Now, MINC files converted from DICOM of Biograph
PET/CT can be viewed on MNI-register, and they look good, though I haven't
checked voxel values in detail yet.

In terms of recording the time dimension, I see dcm2mnc behave differently
from ecattominc. Frame MID times are extracted by dcm2mnc. But, this is a
bit confusing for old Siemens PET users, because frame START times were
extracted by (the good old days) ecattominc. We already have a lot of tools
customized for that.

<mincheader after dcm2mnc>
time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450...
time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180,
180...

So, I would be even more grateful if it could be like:
time = 0, 30, 60, 90....

Is there any good idea to solve or avoid the issue of ambiguity in
recording "time" between dcm2mnc and ecattominc? I am also wondering where
this has come from.

2)    Our PET experiment is consisted of two PET/CT scans on the same day.
They are separated by a 30-min scanning break, and need to be concatenated.
The first scan's frame width is incremental, like typical dynamic PET
scans. The second scan's frame width is constant, 360sec (x 10 frames).
Some header lines that seem to be related to this issue are shown below.

SCAN1(incremental frame time-width)
double time(time) ;
time:start = 15. ;
time:spacing = "irregular" ;
time:alignment = "start_" ;

 time = 15, 45, 75, 105, 135, 165, 210, 270, 330, 390, 450, 570,
    750, 930, 1110, 1350, 1650, 1950, 2250, 2550,.....(truncated)

 time-width = 30, 30, 30, 30, 30, 30, 60, 60, 60, 60, 60, 180, 180, 180,
180,
    300, 300, 300, 300, 300, 300, 300, 300 ;


SCAN2 (360 sec x 10 fr)
double time(time) ;
time:start = 179. ;
time:spacing = "regular__" ;
time:alignment = "start_" ;


 time = 179, 539, 899, 1259, 1619, 1979, 2339, 2699,.....(truncated)

Here, time-with is unavailable in the 2nd scan's header. It would be very
nice if MINC experts could implement an option that forces dcm2mnc to work
in the "irregular" mode, so that the constant time-width would be
explicitly recovered in the 2nd scan's MINC header. In this way, MINC uses
like myself can feel more comfortable, when concatenating two dissimilar
files (after time adjustment, decay correction, head motion correction etc,
of course).

3)    Sometimes, stuck in "Argument list too long". Please help me learn
how to use find and xargs commands properly...

Best regards,
Yoshi

On Fri, Nov 6, 2015 at 1:07 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com>
wrote:

> Hello Yoshi,
>
> I had a similar situation some time ago, I found that I had to rely on
> dcmdump from dcmtk first to split all the DICOM files into individual 3D
> volumes, then run dcm2mnc on each set independently, and finally
> concatenating them with mincconcat along time dimension.
>
>
> On 15-11-05 12:50 AM, Yoshitaka KUMAKURA wrote:
>
>> Dear MINC experts,
>>
>> We would like to use MINC tools to analyze dynamic PET files of a Siemens
>> Biograph mCT 64 PET/CT scanner in an affiliated hospital in Copenhagen. We
>> are not new to MINC, because we are former BIC researchers (currently in
>> Albert Gjedde's lab). But, we are a small PET research group with no
>> computer scientist.
>>
>> We have a favor to ask. We've tried dcm2mnc to convert a set of dynamic 4D
>> PET Dicom files to a minc files, and found that it just makes a 3D minc
>> file, missing the 4th time dimension. Has anybody encountered the same
>> issue? Is a dcm2mnc utility for the scanner available? We are in great
>> need
>> of the minc converter customized for the PET/CT scanner. We would
>> appreciate it very much, if you could find us a solution.
>>
>
>
> --
> Best regards,
>
>  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
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