Hi Giuseppe,
not sure what's going on here. If could be that the first file in the folder
is just a one-file series
and the others are associated to another series.
Just as a test, try deleting the first file in the series from the folder and
reading the series
using vmtkimagereader -ifile MR010001002.dcm
Please send me the output again, we'll go from there.
Thanks!
Luca
On Oct 13, 2011, at 12:18 AM, Giuseppe Isu wrote:
> Hi Luca,
> I paste two different output, got on the vtkOutputWindow and on the command
> line respectively:
> ---------------------------------------------------------------------------------------------------------
> vtkOutputWindow
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Graphics\vtkPlaneSource.cxx, line 386
> vtkPlaneSource (045BF320): Bad plane coordinate system
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Filtering\vtkExecutive.cxx, line 757
> vtkStreamingDemandDrivenPipeline (045BF688): Algorithm
> vtkPlaneSource(045BF320) returned failure for request: vtkInformation
> (045C9988)
> Debug: Off
> Modified Time: 6910
> Reference Count: 1
> Registered Events: (none)
> Request: REQUEST_DATA
> FROM_OUTPUT_PORT: 0
> FORWARD_DIRECTION: 0
> ALGORITHM_AFTER_FORWARD: 1
>
>
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Graphics\vtkPlaneSource.cxx, line 386
> vtkPlaneSource (045D4310): Bad plane coordinate system
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Widgets\vtkImagePlaneWidget.cxx, line
> 1689
> vtkImagePlaneWidget (045D4088): Invalid Y extent: 2.14748e+009
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Graphics\vtkPlaneSource.cxx, line 386
> vtkPlaneSource (045D4310): Bad plane coordinate system
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Filtering\vtkExecutive.cxx, line 757
> vtkStreamingDemandDrivenPipeline (045D4678): Algorithm
> vtkPlaneSource(045D4310) returned failure for request: vtkInformation
> (045DE970)
> Debug: Off
> Modified Time: 7260
> Reference Count: 1
> Registered Events: (none)
> Request: REQUEST_DATA
> FROM_OUTPUT_PORT: 0
> FORWARD_DIRECTION: 0
> ALGORITHM_AFTER_FORWARD: 1
>
> ERROR: In C:\Users\vmtk\local\build\VTK\Graphics\vtkPlaneSource.cxx, line 386
> vtkPlaneSource (045D4310): Bad plane coordinate system
>
> ---------------------------------------------------------------------------------------
> Command Line
>
> C:\Programmi\vmtk 0.9.0>rem @echo off
>
> C:\Programmi\vmtk 0.9.0>set VMTK_DIR=C:\Programmi\vmtk 0.9.0\
>
> C:\Programmi\vmtk 0.9.0>set PATH=C:\Programmi\vmtk
> 0.9.0\bin;C:\Programmi\vmtk 0
> .9.0\lib\InsightToolkit;C:\Programmi\vmtk
> 0.9.0\lib\Python;C:\Programmi\Tecplot\
> Tec360
> 2009\Bin;C:\Python25\;C:\WINXP\system32;C:\WINXP;C:\WINXP\System32\Wbem;C
> :\Programmi\Hummingbird\Connectivity\11.00\Accessories\;C:\Programmi\Hummingbird
> \Connectivity\11.00\NFS
> Maestro\;;C:\Programmi\MATLAB\R2009a\bin;C:\Programmi\MA
> TLAB\R2009a\bin\win32;c:\fluent.inc\ntbin\ntx86
>
> C:\Programmi\vmtk 0.9.0>set PYTHONPATH=C:\Programmi\vmtk
> 0.9.0\lib\site-packages
> ;C:\Programmi\vmtk 0.9.0\lib\vtk-5.6;C:\Programmi\vmtk 0.9.0\lib\vmtk
>
> C:\Programmi\vmtk 0.9.0>cd C:\Programmi\vmtk 0.9.0\
>
> C:\Programmi\vmtk 0.9.0>python bin\vmtk-exe.py
> vmtk> vmtkimagereader -f dicom -d T1 --pipe vmtkimageviewer
> Executing vmtkimagereader -f dicom -d T1 --pipe vmtkimageviewer
>
> Creating vmtkImageReader instance.
> Automatic piping vmtkimagereader
> Parsing options vmtkimagereader
> Format = dicom
> InputDirectoryName = T1
> Explicit piping vmtkimagereader
> Input vmtkimagereader members:
> Id = 0
> Disabled = 0
> Format = dicom
> GuessFormat = 1
> UseITKIO = 1
> Image = 0
> InputFileName =
> InputFilePrefix =
> InputFilePattern =
> InputDirectoryName = T1
> DataExtent = [-1, -1, -1, -1, -1, -1]
> HeaderSize = 0
> DataSpacing = [1.0, 1.0, 1.0]
> DataOrigin = [0.0, 0.0, 0.0]
> DataByteOrder = littleendian
> DataScalarType = float
> FileDimensionality = 3
> Flip = [0, 0, 0]
> AutoOrientDICOMImage = 1
> ImageOutputFileName =
> Executing vmtkimagereader ...
> Reading DICOM directory.
> VTK Orientation: L AI IP
> Flipping: 1 0 1
> Spacing (0.21484375, 0.21484375, 0.0)
> Origin (0.0, 0.0, 0.0)
> Dimensions (512, 304, 1)
> Done executing vmtkimagereader.
> Output vmtkimagereader members:
> Id = 0
> Image = vtkImageData
> RasToIjkMatrixCoefficients = [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
> 0, 1
> ]
> XyzToRasMatrixCoefficients = [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
> 0, 1
> ]
>
> Creating vmtkImageViewer instance.
> Automatic piping vmtkimageviewer
> Image = vmtkimagereader-0.Image
> Parsing options vmtkimageviewer
> Explicit piping vmtkimageviewer
> Input vmtkimageviewer members:
> Id = 0
> Disabled = 0
> Image = vtkImageData
> ImageInputFileName =
> ArrayName =
> vmtkRenderer = None
> WindowLevel = [0.0, 0.0]
> Display = 1
> Margins = 0
> TextureInterpolation = 1
> ContinuousCursor = 0
> ImageOutputFileName =
> Executing vmtkimageviewer ...
> Done executing vmtkimageviewer.
> Output vmtkimageviewer members:
> Id = 0
> Image = vtkImageData
> PlaneWidgetX = vtkImagePlaneWidget
> PlaneWidgetY = vtkImagePlaneWidget
> PlaneWidgetZ = vtkImagePlaneWidget
> vmtk>
>
> ----------------------------------------------------------------------------------------------------
> I thank you so much again. I can't understand what's wrong.
> Best Regards
>
>
>
>
> 2011/10/12 Luca Antiga <luca.ant...@orobix.com>
> Hi Giuseppe,
> can you copy and paste the output you get on the terminal when the pipe is
> running?
> Thanks
>
> Luca
>
>
> On Oct 12, 2011, at 11:57 AM, Giuseppe Isu wrote:
>
>> Hi Luca,
>>
>> first of all thank you for your prompt response.
>>
>> I start from the beginning with the explaination of the problem.
>> I have two different directories of MR dicom images and both of them refer
>> to the same patient. I reckoned that the difference between them is the time
>> of relaxation because the directories are named respectively T1 and T2.
>> Within T1 there's a sequence of images named as follows:
>>
>> MR010001001.dcm, MR011001001.dcm, MR012001001.dcm, ...., MR039001001.dcm
>>
>> for a total of 30 images.
>> Within T2 there are only 5 images named as above starting by MR039001001.dcm
>> to MR043001001.dcm.
>> When I tryed to open the sequence for the first time I copied T1 directory
>> within the vmtk folder and ran the command
>>
>> vmtkimagereader -f dicom -d T1 --pipe vmtkimageviewer
>>
>> and like I said in the previous mail only the first image named
>> MR010001001.dcm opened.
>> I tryed to do what you suggested on a Unix platform
>> I wrote
>>
>> vmtkimagereader -ifile MR010001001.dcm --pipe vmtkimageviewer
>>
>> and the result is the same. The only image opened is this one.
>>
>> Now I think the problem could be clearer to you. I hope what I wrote is
>> enough to find a solution.
>>
>> Thank you in advance
>>
>> Best Regards
>>
>>
>>
>>
>>
>>
>> 2011/10/12 Luca Antiga <luca.ant...@orobix.com>
>> Hi Giuseppe,
>> welcome to vmtk. There shouldn't be any difference between Windows and
>> Unix-like.
>>
>> Can you please post the exact command you are running (not the reference, as
>> you did, but the actual command with the paths)?
>>
>> Also, you may want to try the following:
>> vmtkimagereader -ifile first_file_in_the_series.dcm --pipe vmtkimageviewer
>>
>> It is also possible that your MR dicom directory contains more than one
>> series, so you'll need to separate them beforehands. Just try the above and
>> we'll move from there.
>>
>> Best regards
>>
>>
>> Luca
>>
>>
>> On Oct 11, 2011, at 10:08 PM, Giuseppe Isu wrote:
>>
>>> Hi everybody,
>>> I'm Giuseppe. I'm new to vmtk. Recently I've started to get into it and
>>> I've done all the tutorials. I'm now dealing with a project for which I
>>> need to open a sequence of MR DICOM images in order to reconstruct a
>>> carotid geometry. I use vmtk on a win32 platform and I've already used vmtk
>>> to perform meshes and computing centerlines successfully.
>>> Using the command
>>> vmtkimagereader -f dicom -d "directory_path *" --pipe vmtkimageviewer
>>> where directory_path is my files directory located within the vmtk main
>>> directory.
>>> When I write this command only the first image of the sequence is opened
>>> but I can't understand which is the problem.
>>> Can you give me some tips? Should I try to open these files on a Unix
>>> platform?
>>> Best regards
>>> --
>>> Giuseppe
>>> ------------------------------------------------------------------------------
>>> All the data continuously generated in your IT infrastructure contains a
>>> definitive record of customers, application performance, security
>>> threats, fraudulent activity and more. Splunk takes this data and makes
>>> sense of it. Business sense. IT sense. Common sense.
>>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________
>>> vmtk-users mailing list
>>> vmtk-users@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>>
>> --
>> Giuseppe
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure contains a
>> definitive record of customers, application performance, security
>> threats, fraudulent activity and more. Splunk takes this data and makes
>> sense of it. Business sense. IT sense. Common sense.
>> http://p.sf.net/sfu/splunk-d2d-oct_______________________________________________
>> vmtk-users mailing list
>> vmtk-users@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>
>
>
> --
> Giuseppe
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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