[slicer-users] CLP module passed region: can not change coordinate system

Andriy Fedorov fedorov at bwh.harvard.edu
Thu Apr 15 17:39:49 EDT 2010


I do not think this functionality is supported. See earlier thread here:


You can submit a bug report to mantis
http://www.na-mic.org/Bug/view_all_bug_page.php and describe your
needs and/or inconsistency of the documentation.


On Thu, Apr 15, 2010 at 14:52, Sajendra <sajendra at gmail.com> wrote:
> Hello,
> I am trying to create an excecutable plugin with command line options
> that accepts as input a "region", represented in the slicer GUI as a
> MRMLROINode. I have tested this with Slicer 3.5 (including the latest
> Nightly Build: 2010-04-15) and am having a problem with the coordinate
> system the region is passed in.
> In my XML file I define the region input variable as follows:
> <region coordinateSystem="XXX" multiple="false">
>      <label>Region</label>
>      <name>region</name>
>      <longflag>region</longflag>
>      <description>...</description>
> </region>
> where according to the XML schema
> (http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation#XML_Schema)
> XXX can be set to either "lps","ras", or "ijk". I have found that no
> matter which of the three I choose, the input passed at the command
> line to my module is the same. I am assuming that the coordinates are
> being passed in RAS coordinates as in order to make the region work
> with ITK code within the command line module I have to negate the x
> and y coordinates. Similarly, changing multiple to either true or
> false does not seem to have any effect, but the desired output of that
> attribute is not clear to me, nor documented, so I can't say what the
> exact use of it is. Am I missing something regarding reading the
> region coordinates, or is this a bug where the coordinate system
> attribue is being ignored?
> Thank you,
> Sajendra
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