[Insight-users] Reading images : Visible Woman Eye : Segmentation
validation
Luis Ibanez
luis.ibanez at kitware.com
Sun Oct 31 10:38:31 EST 2004
Hi Gabriele,
Please be more specific.
Your email yesterday said that you read the .mhd
image in ParaView and they only displayed as an outline.
We explained that this was normal and suggested three
options for visualizing the image in ParaView once it
is loaded.
Your email today, says that you cannot read the images
with extension .mhd...,
what *exactly* do you mean when you say that you are
"not able to open the file",
1) does it means that you get an error message while
loading ?
or
2) does it means that after loading you don't see the
image in ParaView ?
Did you read the ParaView manual as we recommended ?
The manual will explain that the filters available
depend on the source that you have selected in the GUI.
It may be easier for you to build the ImageViewer
application from InsightApplications/ImageViewer
and use it for visualizaing the images.
Or... as we recommended yesterday, you could also
use the example
Insight/Examples/IO/
ImageReadImageSeriesWrite.cxx
and convert the .mhd volumes into series of JPEG,
or series of PNG, or series of BMP images.
Please give us a more technical description of your
real problem, so we can have a better idea of how
to help you.
Thanks,
Luis
-----------------------
Gabriele Martino wrote:
> Hi,
> ive tried to open another image,
> *RightEye.vtp* that ive got on itk website, and it correctly opens while im
> not able to open .mhd files(*filter* is disabled on my gui).
> Please could you help me?
>
> ----- Original Message ----- From: "Luis Ibanez" <luis.ibanez at kitware.com>
> To: "Gabriele Martino" <g91182 at libero.it>
> Cc: <insight-users at itk.org>
> Sent: Sunday, October 31, 2004 3:25 AM
> Subject: Re: [Insight-users] Reading images : Visible Woman Eye :
> Segmentation validation
>
>
>>
>> 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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