[MINC-users] mincconcat: 3D->4D or 4D-4D ?

[Robert VINCENT]

Christopher,

It should be harmless to define a step and start for an irregular
dimension.  mincconcat sets the step value for irregular dimensions to a
mean value, which is calculated as (end - begin) / (length - 1), so that
explains the 240 value.  This is actually part of the MINC specification.

	-bert

On Fri, 25 Jun 2004, Christopher Bailey wrote:

>
> Dear MINC-users,
>
> I am trying to concatenate 3D volumes (frames of a dynamic PET scan) into
> a 4D one. Below is the call to mincconcat; I give the frame start times
> and widths with -coordlist and -widhtlist. As you can see, the sampling is
> irregular.
>
> >>>
> mincconcat -clobber -concat_dimension time -coordlist
> "0,15,30,45,60,90,120,180,240,300,450,600,900,1200,1500,1800,2400,3000,3600,4200,4800"
> -widthlist
> "15,15,15,15,30,30,60,60,60,150,150,300,300,300,300,600,600,600,600,600,599"
> /tmp/frame1.mnc /tmp/frame2.mnc /tmp/frame3.mnc /tmp/frame4.mnc
> /tmp/frame5.mnc /tmp/frame6.mnc /tmp/frame7.mnc /tmp/frame8.mnc
> /tmp/frame9.mnc /tmp/frame10.mnc /tmp/frame11.mnc /tmp/frame12.mnc
> /tmp/frame13.mnc /tmp/frame14.mnc /tmp/frame15.mnc /tmp/frame16.mnc
> /tmp/frame17.mnc /tmp/frame18.mnc /tmp/frame19.mnc /tmp/frame20.mnc
> output.mnc
> <<<
>
> Doing a mincinfo on output.mnc, I get
>
> image dimensions: time zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     time                       21          240            0
>     zspace                     63      0.12115            0
>     yspace                    128    0.0845247            0
>     xspace                    128    0.0845247            0
>
> Why is there a step and a start for the time dimension? All the original
> frames were 3D, the starts and widths were given as lists. A mincheader on
> the same files has the following:
> <<<
>         double time(time) ;
>                 time:varid = "MINC standard variable" ;
>                 time:vartype = "dimension____" ;
>                 time:version = "MINC Version    1.0" ;
>                 time:spacing = "irregular" ;
>                 time:alignment = "start_" ;
>                 time:start = 0. ;
>                 time:step = 240. ;
>         double time-width(time) ;
>                 time-width:varid = "MINC standard variable" ;
>                 time-width:vartype = "dim-width____" ;
>                 time-width:version = "MINC Version    1.0" ;
>                 time-width:spacing = "irregular" ;
>                 time-width:filtertype = "square____" ;
> >>>
>
>
> So it realises the spacings are irregular and yet insists on having the
> time:start and
> time:step
> fields! Later in the header the "real" starts and widths appear (as
> "globals"?):
>
> <<<
> data:
>
>  time = 0, 15, 30, 45, 60, 90, 120, 180, 240, 300, 450, 600, 900, 1200,
> 1500,1800, 2400, 3000, 3600, 4200, 4800 ;
>
>  time-width = 15, 15, 15, 15, 30, 30, 60, 60, 60, 150, 150, 300, 300, 300,
>     300, 600, 600, 600, 600, 600, 599 ;
> >>>
>
> Now I'm not sure this will ever cause me problems, but it is a peculiar
> "feature", no? Can I be sure none of the MINC tools get confused about
> this matter, screwing up the timing info?
>
> Best,
>
> Chris Bailey
> Center for Functionally Integrative Neuroscience
> Aarhus General Hospital, Denmark
>
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