Hello Joao,
absolutely not a stupid question.
The issue with MATRIX and BEAUFIX is that the dicom directory contains multiple
series.
The DICOM reader in vmtk is pretty basic, and it will not allow you to select
which series to read.
By the way, you may or may not know that there are two ways of reading DICOM
series in vmtk. One is
vmtkimagereader -f dicom -d a_directory
which was historically the first way being implemented, on top of VTK's DICOM
reader plus some
code to reorient a volume in such a way that right/left is preserved, the other
is
vmtkimagereader -ifile first_file_in_a_series.dcm
which uses the ITK DICOM series reader internally.
Probably with the latter you would succeed in reading one series, but which
series to read would
not be easy to specify.
The easiest way to proceed is to first open the dataset using a DICOM reader,
export the single series
of interest to a directory, and to use either one of the above command lines to
read that series.
There are a bunch of tools that you can use to this end, I here name a few:
- 3DSlicer (www.slicer.org)
- OsiriX (www.osirix-viewer.com - Mac only)
- ezDICOM (http://www.cabiatl.com/mricro/ezdicom/index.html - Windows only)
- DicomBrowser (http://www.nitrc.org/projects/dicom_browser)
If you want to go quick, just use the latter: it's not a full-fledged DICOM
viewer, but if you just need
to look inside DICOM files, see the headers and export series it's handy.
Of course there are a bunch of other tools, but these will get you started.
Best regards
Luca
On Nov 30, 2010, at 12:54 AM, Joao Pinto wrote:
> I am new to vmtk, so I feel I must apologize if this is a "stupid" question
> or if it was answered before.
>
> I have installed the program and now I am learning how to use it. In order to
> do so, I am using the DICOM dataset from http://pubimage.hcuge.ch:8080/
>
> I successfully loaded the INCISIX dental scan. However, others like the
> MATRIX or the BEAUFIX are loaded with all levels set at zero.
>
> I am following the tutorials, which seem very good. The commands I am using
> to open the .dcm datasets is, from within the .dcm folder:
>
> vmtk vmtkimagereader -f dicom -d . --pipe vmtkimageviewer
>
> Am I doing something wrong? Why can't I open the MATRIX and BEAUFIX datasets?
>
> Thank you for your help,
>
> Joao Pinto
>
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