[Insight-users] ImageSeriesReader

Thu, 17 Apr 2003 15:17:50 -0700

Hi Mathias,

You're right -- MRIConvert uses the image position patient and image
orientation patient tags to order the slices along the slice normal.
That's the only way to keep things consistent across scanner software.

Multiple-volume series are handled by checking approprate tags -- right
now I check echo number, acquisition number, and sequence description. I
can add trigger time to that list. I'll let you know when it's done.

Jolinda

> 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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