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

[Robert D. Vincent]

Hi Yoshi,

1. We read the frame times from specific DICOM fields, so it is likely that
the DICOM itself is recording the mid point. Again, if you can provide a
scan, we can change the behavior of the program to record the initial frame
time.

2. This could be easily done, but it should not make any actual difference.
Does mincconcat work properly with the regular/irregular dimensions?

3. You are getting "Argument list too long" when running dcm2mnc? This
should be easily avoidable. You can generally just specify a directory name
for a set of DICOM files:

dcm2mnc <input-directory> <output_directory>

Alternatively, you can read a list of files from standard input:

find <input-directory> -name "*.dcm" | dcm2mnc -stdin <output_directory>

    -bert


On Mon, Nov 9, 2015 at 9:31 AM, Yoshitaka KUMAKURA <yoshi.kumakura at gmail.com
> wrote:

> 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
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
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