You’re welcome. Did you use any of our official binary installers or did you
build MITK from source? In the latter case you should definitely make sure to
set the right 64 bit version of the generator in CMake. We do only support
64bit.
Best,
Stefan
From: Paolo Cabras [mailto:cab...@unistra.fr]
Sent: Donnerstag, 5. April 2018 13:29
To: Dinkelacker, Stefan; Goch, Caspar Jonas; mitk-users@lists.sourceforge.net
Subject: Re: [mitk-users] problem loading dicom
Thank you Stefan.. it seems to be a memory issue related to the fact that 32
bit processes has memory usage limitations.
My OS is 64 bit, then I could extend those limitations without 4GT tuning by
adding /LARGEADDRESSAWARE flag to CMAKE_EXE_LINKER_FLAGS. Could it be the same
problem also in the Workbench ?
I will try on more data set, but for this one - at least - the problem seems to
be solved.
Thank you for your hints !
Paolo
Le 05/apr/2018 à 09:20, Dinkelacker, Stefan a écrit :
Hi, what are the dimensions and pixel type of your slices? Usually you need >
2x the size of RAM. But maybe you have something like a 4 GB restriction for
processes depending on your OS? Have a look at the RAM consumption through the
monitoring of your OS (task manager in Windows, system monitor in Linux). Does
it really increases until it reaches the 32 GB?
Best,
Stefan
From: Paolo Cabras [mailto:cab...@unistra.fr]
Sent: Mittwoch, 4. April 2018 17:56
To: Goch, Caspar Jonas;
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Subject: Re: [mitk-users] problem loading dicom
Hi Caspar,
thank you for the answer! I have tried with MITK workbench but I have the same
problem and, unfortunately, it seems not due to a specific slice, but on the
number of slices I load.
I tested what you suggested in my application with different consecutive slices
and everything works fine in [case2] as far as I load less than 560 slices
(with 567 it does not always work).
I tested the same thing with the MITK Workbench (with drag and drop):
everything works if I load small volumes (<= 280 slices) but this is not the
case If I try to load a bigger (even partial) volume (e.g.: the last 500 files
or the first 300). In this last case, when selecting the MITK DICOM Reader from
the pop-up menu, the same unknown error is returned; whereas, when selecting
the "v2 (autoselect)" option the following message appears in the mbilog window:
875.18 core.mod.dicomReader.dicomSeriesreaderhelper ERROR: Out of memory.
Cannot load DICOM series:
e:\data_lib\mitk\bd-d\ep\include\itk-4.9\itkImportImageContainer.hxx:199:
Failed to allocate memory for image.
Any advice (I have 32GB of RAM)? Thank you again!
Regards,
Paolo
Le 28/mar/2018 à 18:01, Goch, Caspar Jonas a écrit :
Hi Paolo,
Have you tried loading the same data set with a relatively current MITK build?
If you drag and drop one of the files (a single file, not all of them,
otherwise it might try loading it 602 times) and select one of the reader
choices offered by the pop-up menu, what happens?
If you load only the last 72 slices, does the same error happen (it might be a
broken slice, so you could potentially narrow it down to a single file)?
Best,
Caspar
-----Ursprüngliche Nachricht-----
Von: Paolo Cabras [mailto:cab...@unistra.fr]
Gesendet: Mittwoch, 28. März 2018 14:59
An: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
Betreff: [mitk-users] problem loading dicom
Hi everybody,
I am quite new to MITK and I am trying to develop a standalone application that
loads a set of dicom images and render it into a stdMultiWidget (the data set I
am using is composed by 602 slice of
512x512 pixels).
I am using mitk::IOUtil::Load(myFilename, *myDataStorage) and, actually,
everything works fine if [case1] myFilename is given as an argument to my
program and I load the data before showing my QtMainWindow where the
stdMultiWidget is included (exactly as it is done in Step8 of the mitk
examples).
However, it does not work, if [case2] I use the mitk::IOUtil::Load inside a
callback function (a Qt slot) of a File menu action or a pushButton (in this
case myFilename is a std::string hard-coded within the callback function). More
precisely, in [case2] Load is not capable to load the entire 602 slices data
set, but it does work if the input volume is reduced to the first 540 slices.
I do not know if it can be useful, but I had a look at the memory usage of the
process and in [case1] my application has a peak of used memory of about
763.000 K during loading which comes back to 568.000 K after everything has
been rendered. Whereas in [case2] (when trying to load the whole dataset) the
memory usage increase till about 592.000 K before the MITK error is thrown.
Here follows the log of the application with the mentioned error at the end
(the error showed in the first line appears also in [case1], but in that case
everything is correctly rendered afterwards):
Wed Mar 28 13:07:27 2018
7.94 core.mod.cest.customtagparser ERROR: Could not parse empty custom dicom
string
10.65 core.mod.core.dicomSeriesreaderSvc:
--------------------------------------
------------------------------------------
10.66 core.mod.core.dicomSeriesreaderSvc: DicomSeriesReader: Loading DICOM
series 0: Series
UID1.2.392.200036.9116.2.6.1.3268.2056440552.1512124464.240725
10.66 core.mod.core.dicomSeriesreaderSvc: 607 'CT' files (CT Image
Storage) loaded into 1 mitk::Image
10.67 core.mod.core.dicomSeriesreaderSvc: multi-frame: No
10.67 core.mod.core.dicomSeriesreaderSvc: reader support: Supported
10.67 core.mod.core.dicomSeriesreaderSvc: pixel spacing type: In Patient
10.68 core.mod.core.dicomSeriesreaderSvc: gantry tilt corrected: No
10.68 core.mod.core.dicomSeriesreaderSvc: 3D+t: No
10.68 core.mod.core.dicomSeriesreaderSvc:
--------------------------------------
------------------------------------------
20.29 core.mod.core.dicomSeriesreader ERROR: Error encountered when loading
DICOM series:Unknown exception
20.29 core.mod.core.dicomSeriesreaderSvc ERROR: DicomSeriesReader:
Skipping series 0 due to some unspecified error...
20.30 core.mod.core.ioUtil ERROR: Unknown read error occurred reading
E:/Images/Cases/C/C0001
Maybe I should use something as mitkDICOMITKSeriesGDCMReader ? The fact is that
Load seems to recognize the volume, so I am not sure if the problem is the
reader.
Finally, some more details ... I am using windows 7, mitk 2016.11 with Qt
5.7.1 and compiling with msvc2013 32 bit.
I hope I was able to explain the issue... any suggestion would be greatly
appreciated!
Best regards,
--
Paolo Cabras
Research Engineer
Automatic, Vision and Control Team
ICUBE (UMR 7357 CNRS-Université de Strasbourg)
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
mitk-users mailing list
mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/mitk-users
---
This email has been checked for viruses by AVG.
http://www.avg.com
--
Paolo Cabras
Research Engineer
Automatic, Vision and Control Team
ICUBE (UMR 7357 CNRS-Université de Strasbourg)
+33 (0) 3 88 11 90 68
[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png]<http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
Virus-free.
www.avg.com<http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
--
Paolo Cabras
Research Engineer
Automatic, Vision and Control Team
ICUBE (UMR 7357 CNRS-Université de Strasbourg)
+33 (0) 3 88 11 90 68
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
mitk-users mailing list
mitk-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mitk-users
