ITK 10th Anniversary: 3 days to DASHBOARD FEST 1.0 : Nov 5th 9pm EST

[Luis Ibanez]

         The ITK DASHBOARD FEST 1.0

http://www.itk.org/Wiki/ITK_10th_Anniversary_Activities/Dashboard_Fest_1.0

will start on:

         Thursday November 5th at 9pm EST.


Please not that US daylight savings time change
just took place this past Sunday, Nov 1st.


Everyone can participate in the Dashboard Fest !

You just need:

         1) A working computer
         2) An Internet connection


Please see the following Wiki page, for details
http://www.itk.org/Wiki/ITK_10th_Anniversary_Activities/Dashboard_Fest_1.0


Let us know if you find any problems,
while following the preparation instructions.


       Thanks


              Luis
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[phuong trinh pham ngoc]

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Hello everyone,
I have a "series2.raw" file together with it's header file "series2.mhd". The content of this ".mhd" file is as follows:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
ElementSpacing = 0.449 0.449 0.600
DimSize = 512 512 246
ElementType = MET_USHORT
ElementDataFile = series2.raw

This raw file includes many image files as slices. I received this but did not know anything more about how many slices there are in this ".raw " file. I tried to read this ".raw" file by ITK 2.4.8 through both ".raw" file and ".mhd" file. I think I can read it. However, the problem is the work after that. I do not know how to extract the slices in this raw file correctly.

1. I used the code from "Examples/IO/DicomSeriesReadSeriesWrite.cxx" to write multiple slices. It did create 245 images but there is big distorsions in all images (slices). I checked on the internet and retrieved many anwsers. It is said that this was caused by the lack of orientation and etc. I found out that we can correct this problem by setting the metadatadictionaryArray through SetMetaDataDitionaryArray. But I do not know how to do it and how I can get the information of this metadatadictionaryarray. Is MetaDataDictionaryArray the list of all slice filenames? If I know how many slices there are in that raw file, CAN ITK help us to extract corectly?

2. Anyone know how to extract the slices from this ".raw" file correctly? I do not need to save it as DICOM slices. All I need is to extract all slices from this .raw file correctly so that I can have all slices as multi images in normal formats such as JPG, BMP or DICOM.

Thanks in advance! Hope that I can have the answer for this problem which I've tried my best to solve but hopeless :( .
Looking forward to your replies!
Regards,
Phuong Trinh.

---

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[Luis Ibanez]

Hi Phuong,

1) When you read the image using  the .mhd file that you posted,
    ITK is going to read it as a 3D volume (which is good).

2) You can then save the individual slices as DICOM slices,
    if you want. The program that you should use is:

        Insight/Examples/IO/ImageReadImageSeriesWrite.cxx
        if you want to save the slices as JPEG or PNG files.


    or

        Insight/Example/IO/ImageReadDicomSeriesWrite.cxx
        if you want to save the slices as DICOM files.

        and you don't need to worry about the meta data dictionary
        at this point, because you are not reading the image from
        DICOM anyways, so most of the specific tag values are
        actually not available.

3) If you see that the content of the slices look distorted,
    this may indicate that your values of

                         DimSize = 512 512 24

    are not quite correct.

    Please post a screenshot of the distorted images so that
    we can help you identify the source of the problem.



    Thanks


          Luis


-----------------------------------------------------------------------------------
On Tue, Nov 3, 2009 at 7:16 AM, phuong trinh pham ngoc
<equationsupertrinh@...> wrote:

> Hello everyone,
> I have a "series2.raw" file together with it's header file "series2.mhd".
> The content of this ".mhd" file is as follows:
>
> ObjectType = Image
> NDims = 3
> BinaryData = True
> BinaryDataByteOrderMSB = False
> ElementSpacing = 0.449 0.449 0.600
> DimSize = 512 512 246
> ElementType = MET_USHORT
> ElementDataFile = series2.raw
>
> This raw file includes many image files as slices. I received this but did
> not know anything more about how many slices there are in this ".raw " file.
> I tried to read this ".raw" file by ITK 2.4.8 through both ".raw" file and
> ".mhd" file. I think I can read it. However, the problem is the work after
> that. I do not know how to extract the slices in this raw file correctly.
>
> 1. I used the code from "Examples/IO/DicomSeriesReadSeriesWrite.cxx" to
> write multiple slices. It did create 245 images but there is big distorsions
> in all images (slices). I checked on the internet and retrieved many
> anwsers. It is said that this was caused by the lack of orientation and etc.
> I found out that we can correct this problem by setting the
> metadatadictionaryArray through SetMetaDataDitionaryArray. But I do not know
> how to do it and how I can get the information of this
> metadatadictionaryarray. Is MetaDataDictionaryArray the list of all slice
> filenames? If I know how many slices there are in that raw file, CAN ITK
> help us to extract corectly?
>
> 2. Anyone know how to extract the slices from this ".raw" file correctly? I
> do not need to save it as DICOM slices. All I need is to extract all slices
> from this .raw file correctly so that I can have all slices as multi images
> in normal formats such as JPG, BMP or DICOM.
>
> Thanks in advance! Hope that I can have the answer for this problem which
> I've tried my best to solve but hopeless :( .
> Looking forward to your replies!
> Regards,
> Phuong Trinh.
>
>
> ________________________________
> Windows Live Hotmail: Your friends can get your Facebook updates, right from
> Hotmail®.

_____________________________________
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Kitware offers ITK Training Courses, for more information visit:
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Follow this link to subscribe/unsubscribe:
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