[Insight-users] Reading images : Visible Woman Eye : Segmentation validation

[Luis Ibanez]

Hi Gabriele,

Please read the Paraview Users Guide

 http://www.paraview.org/files/v1.6/ParaViewUsersGuide.PDF

It is normal that ParaView will show you only the outline of the
dataset that you loaded.  

Once you load the dataset, you want to use the "Cut" filter
in order to take a slice of the dataset,

                                     or

You can use the "Extract Grid" filter and then in the sliders
that it will display, you can select the slices along X, Y, Z
that you want to visualize.
 
                                     or

Since these images are binary masks, you can also extract their
surfaces with the "Contour" filter.


  Regards,


     Luis


--------------------------------------
Gabriele Martino wrote:

> Hi,
> ive downloaded *Paraview software* but i have also problems. I open 
> *Paraview* then i select *open data* and then i select 
> *11r.raw.cropped.mhd* but image is loded as a simple cube!!
> I think its not what image contains.
>
> Please could you help me?
>
> Martino Gabriele
>
> ----- Original Message ----- From: "Luis Ibanez" 
> <luis.ibanez at kitware.com>
> To: "Gabriele Martino" <g91182 at libero.it>
> Cc: <insight-users at itk.org>
> Sent: Saturday, October 30, 2004 11:31 PM
> Subject: Re: [Insight-users] Reading images : Visible Woman Eye : 
> Segmentation validation
>
>
>>
>> Hi Gabriele,
>>
>> Thanks for letting us know the exact location
>> of the images that you are trying to load.
>>
>>
>> All the files in
>> ftp://public.kitware.com/pub/itk/Data/WatershedSegmentationValidation/ColorVHP/ 
>>
>>
>> are RAW files, and their format is described in the README.txt file.
>>
>>
>>
>> We just created MetaImage files for all the RAW files in the 
>> subdirectories
>>
>>                      ColorVHP/GroundTruth
>>                      ColorVHP/HandSegmentations
>>                      ColorVHP/WSSegmentations
>>
>>
>> The MetaImage header files have extensions .mhd and can be read with the
>> itk::ImageFileReader directly. This means that *any* ITK application 
>> that
>> is capable of loading 3D data, will be able to read these images.
>>
>> In particular, for the segmentations you can use the viewer in
>>
>>        InsightApplications/ImageViewer
>>
>> for the color images you can use the viewer in
>>
>>        InsightApplications/ImageColorViewer
>>     You can also load .mhd file in ParaView. This is an open source
>> application that can be downloaded for free from
>>
>>          http://www.paraview.org
>>
>>
>>
>> For details on the MetaImage format please read the description
>> on the "Data" link of www.itk.org.
>>
>> If you still want ot convert those volume to series of 2D slices
>> then please look at the Example
>>
>>
>>       Insight/Examples/IO/ImageReadImageSeriesWrite.cxx
>>
>>
>> For details on the use of the itk::ImageFileRead class, please read
>> the chapter of the ITK Software Guide
>>
>>        http://www.itk.org/ItkSoftwareGuide.pdf
>>
>> Chapter "Reading and Writing Images".
>>
>>
>>
>> Note that every .mhd file corresponds to a volume. The reason
>> why you find multiple volumes for every structure { eye, lens, rectus,
>> optic nerve} is that the segmentation were done multiple times in
>> order to asses reproducibility.
>>
>>
>>
>>     Regards,
>>
>>
>>         Luis
>>
>>
>> -----------------------------
>> Gabriele Martino wrote:
>>
>>> Hi,
>>> sorry!
>>> The link is 
>>> ftp://public.kitware.com/pub/itk/Data/WatershedSegmentationValidation/ColorVHP/ 
>>>
>>>
>>> id like to have, in other formats(bmp,tiff, gif,jpeg) ,
>>> images that are in the folders "Hand Segmentation"
>>> and "WSSegmentations" and also images that are in "Groundtruth" to 
>>> test my segmentations.
>>>
>>> Thanks a lot :-)
>>>
>>> Martino Gabriele
>>>
>>> ----- Original Message ----- From: "Luis Ibanez" 
>>> <luis.ibanez at kitware.com>
>>> To: "Gabriele Martino" <g91182 at libero.it>
>>> Sent: Saturday, October 30, 2004 6:01 PM
>>> Subject: Re: [Insight-users] Reading images
>>>
>>>
>>>>
>>>> Hi Gabriele,
>>>>
>>>> We will be glad to help you read the images.
>>>>
>>>> However, it will be easier if you answer our question
>>>> and tell us *exactly* what image are you trying to read.
>>>>
>>>> Please be more specific, there are *a lot* of different images
>>>> in the FTP site.
>>>>
>>>>
>>>>   Thanks,
>>>>
>>>>
>>>>       Luis
>>>>
>>>>
>>>> ------------------------------
>>>> Gabriele Martino wrote:
>>>>
>>>>> hi,
>>>>> i cant read image. i get only black images!
>>>>>
>>>>> Can u read thet for me?
>>>>>
>>>>> thank a lot
>>>>>
>>>>> ----- Original Message ----- From: "Luis Ibanez" 
>>>>> <luis.ibanez at kitware.com>
>>>>> To: "Gabriele Martino" <g91182 at libero.it>
>>>>> Cc: <insight-users at itk.org>
>>>>> Sent: Saturday, October 30, 2004 12:34 AM
>>>>> Subject: Re: [Insight-users] Reading images
>>>>>
>>>>>
>>>>>>
>>>>>> Hi Gabriele,
>>>>>>
>>>>>> By "raw.cropped" are you making reference to the
>>>>>> VisibleWoman slices in the FTP site ?
>>>>>>
>>>>>> The best way to read RAW data is to write a MetaImage
>>>>>> header for it.
>>>>>>
>>>>>> You will find instructions on how to do this in the
>>>>>> "Data" link:
>>>>>>
>>>>>>       http://www.itk.org/HTML/Data.htm
>>>>>>
>>>>>> You should also read the IO chapter of the ITK
>>>>>> software guide
>>>>>>
>>>>>>     http://www.itk.org/ItkSoftwareGuide.pdf
>>>>>>
>>>>>> Is the chapter entitled "Reading and Writing Images".
>>>>>>
>>>>>>
>>>>>> Please let us know if you have further questions,
>>>>>>
>>>>>>
>>>>>>   Thanks
>>>>>>
>>>>>>
>>>>>>     Luis
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----------------------
>>>>>> Gabriele Martino wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> i need some images with groundtruth to test my software. ive 
>>>>>>> found some datas on itk website.
>>>>>>> How can i read images raw.cropped? are they avaible in other 
>>>>>>> formats? Can everyone read them for me?
>>>>>>>  Thanks a lot.
>>>>>>>  Martino Gabriele
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------ 
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Insight-users mailing list
>>>>>>> Insight-users at itk.org
>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
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