Fwd: [Insight-users] Analyze_Series2
Luis Ibanez
luis.ibanez at kitware.com
Mon Dec 13 12:20:13 EST 2004
Hi Yasser,
Thanks for clarifying the source of your images.
After downloading the data directly from the IBSR site
we checked the content of these images and found the
following:
1) They are *not* in Analyze fileformat.
The files are just "RAW" images as it is indicated
in the README file provided by the IBSR site.
The fact that they are using a .img extension is
certainly misleading...
2) The images are using pixel type: signed short
3) The images have different spacing, the values
are specified in the README file. Although they
appear as "slice thickness", it seems to actually
be the "slice spacing".
We have created MetaImage headers for all the volumes in
the group that you are working on.
Please find all these MetaImage headers in the attached
tgz file.
You *must* put each one of the .mhd files along with the
corresponding .img files. MetaImage expects to find the
RAW files in the *same* directory where the .mhd file is.
Please let us know if you find any further problem
reading the IBSR images with ITK.
Thanks,
Luis
---------------------
yasser salman wrote:
> ------------------------------------------------------------------------
>
> Subject:
> Re: Fwd: [Insight-users] Analyze_Series
> From:
> yasser salman <yass71 at yahoo.com>
> Date:
> Tue, 7 Dec 2004 12:29:01 -0800 (PST)
> To:
> Luis Ibanez <luis.ibanez at kitware.com>
>
>
> Hi luis..,
>
> If u plz about ur request to send u Images to ge them
> a try , As u know i can't sent more than 40K in ITK
> mail box, any way My Data come from IBSR (Realdata
> ->Single subject with tumor, multiple scans over time,
> T1-Weighted Scans with Gadolinium->series
> 1,10,13,21,26,31,37),
> so plz give them a try to know what's my problem.,
> N.B : these data give a good result in VolView when
> i'm give them a try.,
> thanks luis,,
> yasser
> --- Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>
>>Hi Yasser
>>
>>1) The elements of the argv array are pointers to
>>chars
>> that have been assigned from the strings in the
>>arguments
>> of the command line.
>>
>> If you assign new values to such pointers you
>>will not
>> be able to recover the original values from the
>>command
>> line.
>>
>> If you need strings for holding the filenames of
>>your
>> images you should simply use the std::string
>>class.
>>
>>
>>2) From the message of itkAnalyzeImageIO class, it
>>seems that
>> your images do not fit correctly in the analyze
>>format.
>> could you please make available one (or several)
>>of such
>> images so we can give them a try ?
>>
>>
>>3) Please double check that all the image files are
>>in the
>> directory that you specified and that you have
>>*permission*
>> for reading all of them.
>>
>>
>>
>>Regards,
>>
>>
>>
>> Luis
>>
>>
>>
>>---------------------
>>yasser salman wrote:
>>
>>
>>>Hi luis,
>>>thanks for ur notes., but what's the difference
>>
>>when i
>>
>>>assign constat values in my code or read it from a
>>>command line?,
>>>1- my error message is
>>>"itk::ExceptionObject <00F8FBFC>
>>>Location :"Unknown"
>>>File:
>>>
>>
>>D:\InsightToolKit-1.6.0\Code\IOitkAnalyzeImageIO.cxx
>>
>>>Line:862
>>>Description: File cannot be read.
>>>
>>>2- i add this to my code and it print all of them
>>>correctly,
>>>
>>>std::vector<std::string> names =
>>>nameGenerator->GetFileNames();
>>> std::vector<std::string>::iterator nit;
>>>
>>> for (nit = names.begin();
>>> nit != names.end();
>>> nit++)
>>> {
>>> std::cout << "File: " << (*nit).c_str() <<
>>>std::endl;
>>> }
>>>
>>>thanks luis,,.
>>>Regards
>>>yasser..,
>>>
>>>--- Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>
>>>
>>>
>>>>Hi Yasser,
>>>>
>>>>
>>>>Please *NEVER* assign values to the component of
>>
>>the
>>
>>>>"argv[]" array.
>>>>
>>>>These strings are read from the command line, they
>>>>actually should be
>>>>treated as "const".
>>>>
>>>>
>>>>It is unfortunate that the compiler allowed you to
>>>>do something like:
>>>>
>>>>
>>argv[1]="C:/YASCOPY/ImageData/126_1/126_1_1.img";
>>
>>>>argv[2]="C:/YASCOPY/ImageData/126_1/126_1_28.img";
>>>>
>>>>>argv[3]="C:/YASCOPY/ImageData/126_1/Out";
>>>>
>>>>
>>>>
>>>>Please post the exact error message that you get.
>>>>You are probably
>>>>getting also the filename of the file that cannot
>>
>>be
>>
>>>>read.
>>>>
>>>>It is a common mistake to provide a wrongly
>>>>constructed printf format
>>>>to the filenames generator.
>>>>
>>>>For double checking the names that you are
>>>>generating, you can get
>>>>the container returned by the GetFileNames()
>>
>>method
>>
>>>>of the filename
>>>>generator, and print all of them. Please look at
>>>>the Doxigen
>>>>documentation of the NumericSeriesFileNames class:
>>>>
>>>>
>>>
>>>
> http://www.itk.org/Insight/Doxygen/html/classitk_1_1NumericSeriesFileNames.html
>
>>>>
>>>> Regards,
>>>>
>>>>
>>>>
>>>> Luis
>>>>
>>>>
>>>>
>>>>----------------------
>>>>yasser salman wrote:
>>>>
>>>>
>>>>
>>>>>oops , i forgot the File, sorry, i attached it
>>
>>now
>>
>>>>>Note: forwarded message attached.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>__________________________________
>>>>>Do you Yahoo!?
>>>>>The all-new My Yahoo! - What will yours do?
>>>>>http://my.yahoo.com
>>>>>
>>>>>
>>>>>
>>>>
> ------------------------------------------------------------------------
>
>>>>>Subject:
>>>>>[Insight-users] Analyze_Series
>>>>>From:
>>>>>yasser salman <yass71 at yahoo.com>
>>>>>Date:
>>>>>Mon, 29 Nov 2004 12:32:52 -0800 (PST)
>>>>>To:
>>>>>insight-users at itk.org
>>>>>
>>>>>
>>>>>hi all..,
>>>>>i modified the attachment file to read Analyze
>>>>
>>>>image ,
>>>>
>>>>
>>>>>the following Error message appeared " File
>>
>>cannot
>>
>>>>be
>>>>
>>>>
>>>>>read"
>>>>>i'm using Example found in IO directory, but i
>>>>
>>>>think i
>>>>
>>>>
>>>>>have a problem
>>>>>in specify my series location also the output
>>>>
>>>>image
>>>>
>>>>
>>>>>location (and name) can if u plz help me to fix
>>>>
>>>>the
>>>>
>>>>
>>>>>problem.
>>>>>Note: my seires from ISBR and have no header,
>>>>>start slice 126_1_1.img End slice 126_1_28.img
>>
> === message truncated ===
>
>
>
>
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