[Insight-users] ImageSeriesReader

Mon, 21 Apr 2003 09:12:46 -0700

Hi Matthias,

I added "trigger time" to the list of things that identify volumes in a
series. Could you try out the new version? I don't have any 4D cardiac
sequences to test it on (we have a head-only machine), so I'd appreciate
you letting me know if it works.

Thanks,

Jolinda

----- Original Message -----
From: "Mathias Seitel" <mathiasseitel@yahoo.de>
To: "Jolinda Smith" <jolinda@darkwing.uoregon.edu>
Cc: <insight-users@public.kitware.com>
Sent: Wednesday, April 16, 2003 8:04 AM
Subject: Re: [Insight-users] ImageSeriesReader

> Hi Jolinda,
>
> The software worked fine, and the new functionality
> for specifying any required tags is really nice.
> However I'm somewhat confused as to how the individual
> slices of a DICOM series are assembled in the RAW
> file.
>
> Specifically, I've got a 4D-MRI cardiac volume series,
> depicting one cardiac cycle in 3D. It consists of 400
> slices in total, 16 for each volume (thus 25 cardiac
> phases). The image numbers range from 1 to 400. The
> volume of the first cardiac phase consist of images 1,
> 26, 51, the second volume of images 2, 27, 52 and so
> on.
>
> MRIConvert extracts just the first volume (1, 26, ...,
> 376), thus the resulting RAW file is 2 MB in size (256
> x 256 x 16 Bit). I'm wondering how the program knows
> just which slices to use for the volume, skipping the
> remaining 24 each time. Since no Slice Location tag is
> provided in the DICOM files, all I can figure out
> would be either use the z-coordinate of the Image
> Posistion Patient tag, or the Trigger Time tag, both
> of which could be used to correctly identify the
> individual volumes. Or am I ignoring something?
>
> On the other hand, would it be possible to extract not
> only the first volume, but all volumes of the 4D data
> set? This would be a very convenient solution...
>
> Thanks,
> Mathias
>
>
>  --- Jolinda Smith <jolinda@darkwing.uoregon.edu>
> schrieb: > Okay, it's finally done. You can now use
> MRIConvert
> > to create metaimage
> > headers without raw files, and can save any known
> > DICOM tag to the
> > header. Check it out:
> > http://lcni.uoregon.edu/~jolinda/MRIConvert.html.
> > Let me know if you have any trouble -- the new
> > version hasn't exactly
> > been thoroughly tested. BTW, if there's a tag you
> > need to save that
> > isn't in the list, just add it to the "generic.txt"
> > file. It's not a
> > complete list of DICOM tags, just the most common
> > ones for MR images.
> >
> > Jolinda
> >
> > ----- Original Message -----
> > From: "Mathias Seitel" <mathiasseitel@yahoo.de>
> > To: "Jolinda Smith" <jolinda@darkwing.uoregon.edu>
> > Cc: "insight users"
> > <insight-users@public.kitware.com>
> > Sent: Friday, March 21, 2003 6:10 AM
> > Subject: Re: [Insight-users] ImageSeriesReader
> >
> >
> > > Hi Jolinda,
> > >
> > > For our purpose image modality and study/series
> > UIDs
> > > would probably be needed in addition. Rescale
> > > slope/intercept and window width/center or LUT
> > would
> > > also be useful, but I'm not sure if this is
> > required.
> > >
> > > Would it be possible to create a meta image header
> > for
> > > the DICOM files directly, without the intermediate
> > RAW
> > > file? I'm looking for a way to let the user just
> > > select the set of DICOM files he wants to load.
> > >
> > > Thanks,
> > > Mathias
> > >
> > >  --- Jolinda Smith <jolinda@darkwing.uoregon.edu>
> > > schrieb: > Currently, I'm not saving all possible
> > > metaimage
> > > > tags in the header,
> > > > just the ones I need for my own purposes. Let me
> > > > know what information
> > > > you need from the DICOM file, and if there are
> > > > corresponding metaimage
> > > > tags available, I'll add them to the converter.
> > > >
> > > > ----- Original Message -----
> > > > From: "Mathias Seitel" <mathiasseitel@yahoo.de>
> > > > To: <insight-users@public.kitware.com>
> > > > Sent: Wednesday, March 19, 2003 4:47 AM
> > > > Subject: Re: [Insight-users] ImageSeriesReader
> > > >
> > > >
> > > > > Hi Jolinda,
> > > > >
> > > > > thanks alot for your program, it really is a
> > nice
> > > > > tool. I tried it with some of my samples and
> > it
> > > > worked
> > > > > fine, also reading its output with ITK.
> > However
> > > > I'm
> > > > > still undecided on how to proceed. Doing it
> > this
> > > > way
> > > > > may well be an option, but on the other hand
> > in
> > > > order
> > > > > to access additional DICOM info I'll still
> > have to
> > > > > read the DICOM header(s) of the original
> > file(s).
> > > > But
> > > > > first I have to see how many DICOM header
> > > > information
> > > > > is actually needed in the project.
> > > > >
> > > > > Best regards,
> > > > > Mathias
> > > > >
> > > > >  --- Jolinda Smith
> > <jolinda@darkwing.uoregon.edu>
> > > > > schrieb: > Hi Mathias,
> > > > > >
> > > > > > Is the reason you don't want to write meta
> > image
> > > > > > headers for each volume
> > > > > > due to the number of files you'd have to
> > create?
> > > > Or
> > > > > > some other reason? I
> > > > > > have a Windows program that batch converts
> > DICOM
> > > > > > files into metaimage
> > > > > > volumes that works well with large numbers
> > of
> > > > files.
> > > > > > Currently it saves
> > > > > > the image data in a *.raw file, but I could
> > add
> > > > an
> > > > > > option to save meta
> > > > > > image headers only. You can download it at
> > > > > > http://lcni.uoregon.edu/~jolinda/MRIConvert.
> > > > > >
> > > > > > I'd also like to know more about the
> > > > > > ImageSeriesReader. Any change it'll
> > > > > > handle the Siemens' mosaic format?
> > > > > >
> > > > > > Jolinda
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
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