[Insight-users] Convert NRRD into DICOM
Bill Lorensen
bill.lorensen at gmail.com
Sun Jul 5 08:19:27 EDT 2009
Luis,
I just verified that nrrd can only handle unix style "/" slashes in
filenames. It cannot handle windows "\" separators in filenames.
I looked quickly at the nrrd code and it's not obvious how to fix
this. However, I can easily fix the problem in itkNRRDImageIO.cxx by
using itksys::SystemTools::ConvertToUnixSlashes(). I tried this and
the test program now works with "\" in the filenames.
What do you think?
Bill
On Sun, Jul 5, 2009 at 7:50 AM, Bill Lorensen<bill.lorensen at gmail.com> wrote:
> I think I can reproduce the problem.
>
> I just ran itkIOTests itkNrrdImageReadWriteTest with one of the itk
> testing datasets. When I specified the name with forward slash
> separators, the test worked. When I specified with "\" backslash
> separators if failed.
>
> Ezequiel, Can you try this command line:
> C:\Projects\ConversionTool\build\Debug\ConvertIntoDicomSeries.exe
> C:/Downloads/MS-Lesion-Segmentation-2008/Testing-Data/CHB_test1_Part1/CHB_test1_Case01/CHB_test1_Case01_FLAIR.nhdr
> C:/Desktop/
>
> Bill
>
>
> On Sat, Jul 4, 2009 at 3:51 PM, Luis Ibanez<luis.ibanez at kitware.com> wrote:
>>
>> Hi Ezequiel,
>>
>> Thanks for the additional information.
>>
>> Your image of 512 x 512 x 512 short pixels
>> would require:
>>
>>
>> 256 Mb
>>
>>
>> which doesn't seem to be too demanding...
>>
>>
>> So...
>> your suspicion that the problem relates to locating
>> the file itself, sounds reasonable.
>>
>>
>>
>> A typical suspect would be the logic that constructs
>> the filename "fname".
>>
>>
>>
>> Could you please help us debug this problem ?
>>
>>
>> Please do the following:
>>
>>
>> Compile ITK and your program in Debug mode.
>>
>> Put a break point in
>>
>> Insight/Utilities/NrrdIO/formatNRRD.c
>>
>> in line : 113:
>>
>> fname = (char*)malloc(airStrlen(nio->path) + strlen("/") + maxl + 1);
>>
>> Then track the composition of "fname" through the
>> subsequent lines.
>>
>> Somewhere in between 113 and 160 there should be a logic
>> flaw on the construction of the raw data filename.
>>
>>
>> Pay particular attention to line 138-144:
>>
>>
>> if (_NEED_PATH(nio->dataFNFormat)) {
>> strcpy(fname, nio->path);
>> strcat(fname, "/");
>> sprintf(fname +
>> strlen(nio->path) +
>> strlen("/"), nio->dataFNFormat, ii);
>> } else {
>> sprintf(fname, nio->dataFNFormat, ii);
>> }
>>
>>
>> (e.g. including whath
>> path of the "if" in line 138 the code is taking.
>>
>>
>> or whether the code enters the section 149-153:
>>
>>
>> if (_NEED_PATH(nio->dataFN[nio->dataFNIndex])) {
>> sprintf(fname, "%s/%s", nio->path, nio->dataFN[nio->dataFNIndex]);
>> } else {
>> strcpy(fname, nio->dataFN[nio->dataFNIndex]);
>> }
>>
>>
>> Please let us know what you find to be the sequence
>> of lines (in the code) that your program follows when
>> constructing "fname".
>>
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>> ----------------------------
>> Ezequiel Geremia wrote:
>>>
>>> Hi,
>>>
>>>
>>> Thank you, I appreciate your support on this question.
>>>
>>>
>>> The images are volumes dimensions: ( 512, 512, 512 ) and pixel type is
>>> short.
>>>
>>>
>>> While trying to run the task manager with the ITK conversion executable
>>> there is no jump in RAM usage, this is why I think the RAW volume is not
>>> even loaded in memory, the reader just does not find it.
>>>
>>>
>>> My understanding is that there is no memory problem, indeed I manage to
>>> load the same image with the same executable just by moving to the directory
>>> containing the NRRD volumes.
>>>
>>>
>>> Many thanks,
>>>
>>>
>>> Ezequiel
>>>
>>>
>>> *From:* Luis Ibanez [mailto:luis.ibanez at kitware.com]
>>> *Sent:* 02 July 2009 23:56
>>> *To:* Ezequiel Geremia
>>> *Cc:* itk
>>> *Subject:* Re: [Insight-users] Convert NRRD into DICOM
>>>
>>>
>>>
>>> Hi Ezequiel,
>>>
>>> Thanks for posting the error message from the Exception.
>>>
>>> I just verified that a NRRD header file can be moved along
>>> with its associated .raw file to a different directory and still
>>> be read with the NRRD reader included into ITK.
>>>
>>> --
>>>
>>>
>>> Looking at the code...
>>>
>>> ...(Ah!, the Unbeatable Glory of Open Source)...
>>>
>>> We find that the error message that you posted is being
>>> generated by line 161 of:
>>>
>>> Insight/Utilities/NrrdIO/formatNRRD.c
>>>
>>> that curiously is part of (160-165):
>>>
>>> if ((err = (char*)malloc(strlen(fname) + AIR_STRLEN_MED))) {
>>> sprintf(err, "%s: couldn't open \"%s\" (data file %d of %d) for
>>> %s",
>>> me, fname, nio->dataFNIndex+1, (int)_nrrdDataFNNumber(nio),
>>> reading ? "reading" : "writing");
>>> biffAdd(NRRD, err); free(err);
>>> }
>>>
>>>
>>>
>>> Admittedly,
>>> the error message is quite misleading here...
>>>
>>> It is clear that what is happening in these lines above
>>> is that the code is failing to allocate enough memory
>>> for your image.
>>>
>>> So...
>>> please tell us:
>>>
>>>
>>> A) How big is the image ?
>>>
>>> B) How much RAM do you have ?
>>>
>>> and please run this code while you have open the
>>> TaskManager, and check on how much memory
>>> is available at the time the program post this message.
>>>
>>>
>>> If memory allocation turns out to be the real problem,
>>> please feel free to add a bug report suggesting
>>> that this error message be replaced with something
>>> that indicates that we are dealing with a Memory
>>> Allocation problem, as opposed to an I/O problem.
>>>
>>> You can report bugs at:
>>> http://public.kitware.com/Bug/my_view_page.php
>>>
>>>
>>>
>>>
>>> Please let us know what you find,
>>>
>>>
>>> Thanks
>>>
>>>
>>> Luis
>>>
>>>
>>>
>>> -----------------------------------------------------------------------------
>>>
>>> On Thu, Jul 2, 2009 at 1:31 PM, Ezequiel Geremia <t-egerem at microsoft.com
>>> <mailto:t-egerem at microsoft.com>> wrote:
>>>
>>> Hi Luis,
>>>
>>> The reader.Update() call is inside a try\catch block.
>>>
>>> Here is the exception which is caught:
>>>
>>> ExceptionObject caught !
>>>
>>> itk::ExceptionObject (00A0E9A8)
>>> Location: "void __thiscall itk::NrrdImageIO::ReadImageInformation(void)"
>>> File: ..\..\..\src\Code\IO\itkNrrdImageIO.cxx
>>> Line: 264
>>> Description: itk::ERROR: NrrdImageIO(025D1DC0): ReadImageInformation:
>>> Error read
>>> ing C:\Downloads\MS-Lesion-Segmentation-2008\Extracted-Files\Test
>>> ing-Data\CHB_test1_Part1\CHB_test1_Case01\CHB_test1_Case01_FLAIR.nhdr:
>>> [nrrd] nrrdLoad: trouble reading "C:\Downloads\MS-Lesion-Segmenta
>>>
>>> tion-2008\Extracted-Files\Testing-Data\CHB_test1_Part1\CHB_test1_Case01\CHB_test
>>> 1_Case01_FLAIR.nhdr"
>>> [nrrd] nrrdRead: trouble reading NRRD file
>>> [nrrd] _nrrdFormatNRRD_read: couldn't open the first datafile
>>> [nrrd] nrrdIoStateDataFileIterNext: couldn't open
>>> "./CHB_test1_Case01_FLAIR.raw"
>>> (data file 1 of 1) for reading
>>>
>>> In this case, the reader does not seem to add the path of the header file
>>> (i.e.
>>> "C:\Downloads\MS-Lesion-Segmentation-2008\Extracted-Files\Testing-Data\CHB_test1_Part1\CHB_test1_Case01\")
>>> to the filename found in the header file and which is in the same directory
>>> (i.e. "./CHB_test1_Case01_FLAIR.raw").
>>>
>>> Many thanks,
>>>
>>>
>>> Ezequiel
>>>
>>> -----Original Message-----
>>> From: Luis Ibanez [mailto:luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>]
>>>
>>> Sent: 02 July 2009 17:51
>>> To: Ezequiel Geremia; Insight Users
>>> Subject: Re: [Insight-users] Convert NRRD into DICOM
>>>
>>>
>>> Hi Ezequiel,
>>>
>>> Thanks for the update.
>>>
>>> I haven't seen this problem before.
>>>
>>> I would be very surprised if the reader relies on absolute
>>> paths, because that will mean that it is impossible to
>>> move NRRD files from one computer to another,... and even
>>> from one directory to another in the same machine.
>>>
>>>
>>>
>>> Did you got an error message ?
>>>
>>> If so,
>>> Could you please post it to the mailing list ?
>>>
>>> Are you placing the Update() call of the reader
>>> inside a try/catch block ?
>>>
>>>
>>>
>>> Please let us konw
>>>
>>>
>>> Thanks
>>>
>>>
>>> Luis
>>>
>>>
>>> ------------------------
>>> Ezequiel Geremia wrote:
>>> > Hi Luis,
>>> >
>>> > Thank you for answering my mail,
>>> >
>>> > I managed to read NRRD format by passing the header .nhdr or .mhd files
>>> and to convert them into DICOM series.
>>> >
>>> > The NRRD format I got form the MS Segmentation Challenge 2008 & Liver
>>> Tumor Segmentation Challenge 2008 websites seem to be specified as the union
>>> of a header and a RAW data file.
>>> >
>>> > However I experienced another issue concerning the reader. When I pass
>>> the header, which contains the relative filename of the .raw file to be
>>> converted, as an input, the reader is not able to find it (maybe because the
>>> reader relies on absolute filenames).
>>> >
>>> > Do you know a way out of this ?
>>> >
>>> > Regards,
>>> >
>>> > Ezequiel
>>> >
>>> >
>>> >
>>> > -----Original Message-----
>>> > From: Luis Ibanez [mailto:luis.ibanez at kitware.com
>>> <mailto:luis.ibanez at kitware.com>]
>>> > Sent: 30 June 2009 22:27
>>> > To: Ezequiel Geremia
>>> > Cc: insight-users at itk.org <mailto:insight-users at itk.org>
>>> > Subject: Re: [Insight-users] Convert NRRD into DICOM
>>> >
>>> >
>>> >
>>> > Hi Ezequiel,
>>> >
>>> >
>>> > If your input file is in NRRD format,
>>> > why are you passing a RAW format as input ?
>>> >
>>> >
>>> > ITK is expecting that a NRRD file will be called
>>> >
>>> > LTS_IMG05.nrrd
>>> >
>>> > not to be called:
>>> >
>>> > LTS_IMG05.raw
>>> >
>>> >
>>> >
>>> > Also, is this image 2D or 3D ?
>>> >
>>> >
>>> > You may have to retouch the example code in order
>>> > to manage 3D images.
>>> >
>>> >
>>> > Regards,
>>> >
>>> >
>>> > Luis
>>> >
>>> >
>>> > --------------------------
>>> > Ezequiel Geremia wrote:
>>> >
>>> >>Hi,
>>> >>
>>> >>
>>> >>
>>> >>I tried to convert NRRD, which is ITK supported format, data volumes
>>> >>into DICOM volumes using the generic converter given in
>>> >>/ImageReadWrite.exe/ with the following arguments
>>> >>
>>> >>- Input file: LTS_IMG05.raw
>>> >>
>>> >>- Output file: LTS_IM05.dcm (also tried .dic and .dicom file
>>> >>extensions)
>>> >>
>>> >>- Exception:
>>> >>
>>> >>itk::ImageFileReaderException (0146EEC0)
>>> >>
>>> >>Location: "void __thiscall itk::ImageFileReader<class
>>> >>itk::Image<short,3>,class itk::DefaultConvertPixelTraits<short>
>>> >> >::GenerateOutputInformation(void)"
>>> >>
>>> >>File:
>>>
>>> >>c:\users\t-egerem\software\insighttoolkit-3.14.0\src\code\io\itkImageFileReader.txx
>>> >>
>>> >>Line: 144
>>> >>
>>> >>Description: Could not create IO object for file
>>>
>>> >>C:\Users\t-egerem\Downloads\3D-Liver-Tumor-Segmentation-Challenge-2008\Extracted-Files\Testing-Data\LTS_IMG05.raw
>>> >>
>>> >> Tried to create one of the following:
>>> >>
>>> >> GDCMImageIO
>>> >>
>>> >> MetaImageIO
>>> >>
>>> >> PNGImageIO
>>> >>
>>> >> VTKImageIO
>>> >>
>>> >> GiplImageIO
>>> >>
>>> >> BioRadImageIO
>>> >>
>>> >> LSMImageIO
>>> >>
>>> >> AnalyzeImageIO
>>> >>
>>> >> NiftiImageIO
>>> >>
>>> >> StimulateImageIO
>>> >>
>>> >> JPEGImageIO
>>> >>
>>> >> TIFFImageIO
>>> >>
>>> >> NrrdImageIO
>>> >>
>>> >> BMPImageIO
>>> >>
>>> >> DICOMImageIO2
>>> >>
>>> >> You probably failed to set a file suffix or set the suffix to an
>>> >>unsupported type.
>>> >>
>>> >>
>>> >>
>>> >>Then I tried to shortcut the pluggable factory mechanism and it does
>>> not
>>> >>as well with the same data it throws the following error message
>>> >>
>>> >> itk::ExceptionObject (0122F614)
>>> >>
>>> >>Location: "void __thiscall itk::ImageFileReader<class
>>> >>itk::Image<short,3>,class itk::DefaultConvertPixelTraits<short>
>>> >> >::EnlargeOutputRequestedRegion(class itk::DataObject *)"File:
>>>
>>> >>c:\users\t-egerem\software\insighttoolkit-3.14.0\src\code\io\itkImageFileReader.txx
>>> >>
>>> >>Line: 342
>>> >>
>>> >>Description: itk::ERROR: ImageFileReader(0172F7C0): ImageIO returns IO
>>> >>region that does not fully contain the requested regionRequested
>>> region:
>>> >>ImageRegion (0122F8D8)
>>> >>
>>> >> Dimension: 3
>>> >>
>>> >> Index: [0, 0, 0]
>>> >>
>>> >> Size: [0, 0, 0]
>>> >>
>>> >>StreamableRegion region: ImageRegion (0172F8A4)
>>> >>
>>> >> Dimension: 3
>>> >>
>>> >> Index: [0, 0, 0]
>>> >>
>>> >> Size: [0, 0, 0]
>>> >>
>>> >>
>>> >>
>>> >>If you can think of a solution can you please point it out to me ?
>>> >>
>>> >>
>>> >>
>>> >>Regards,
>>> >>
>>> >>
>>> >>
>>> >>Ezequiel Geremia
>>> >>
>>> >>
>>> >>
>>> >>
>>>
>>> >>------------------------------------------------------------------------
>>> >>
>>> >>_____________________________________
>>> >>Powered by www.kitware.com <http://www.kitware.com>
>>> >>
>>> >>Visit other Kitware open-source projects at
>>> >>http://www.kitware.com/opensource/opensource.html
>>> >>
>>> >>Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>> >>
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>>> >>http://www.itk.org/mailman/listinfo/insight-users
>>> >
>>> >
>>> >
>>>
>>>
>>
>> _____________________________________
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>>
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