[Insight-users] IBSR Data

[Luis Ibanez]

Hi Yasser,

You can read series of slices into a 3D volume
by using the ImageSeriesReader class

http://www.itk.org/Insight/Doxygen/html/classitk_1_1ImageSeriesReader.html

You will find examples on the use of this class
in the directory

    Insight/Examples/IO/
             DicomSeriesReadImageWrite.cxx
             DicomSeriesReadImageWrite2.cxx
             ImageReadImageSeriesWrite.cxx
             ImageSeriesReadWrite.cxx
             RGBImageSeriesReadWrite.cxx


Regards,


     Luis



--------------------
yasser salman wrote:

> Hi Lydia ,
> about ur suggestion for reading Analyze *.img using
> Osiris, and then convert them to DICOM format , how
> can i read them "all" Using
>  header file ( i can read it slice by slice but i
> think it's not a smart jop to read it in this way and
> convert each slice after read to .dcm format), i
> create this header for the series 126_1.img (scans
> over time) but it dosn't work with Osiris,  volview 
> and 3D doctor , the file name is "126_1.mhd", can u
> help me to correct the error here., 
> Also., can i ask Luis to help me to read these files
> in ITK and convert them to *dcm format ,, thanks all,
> and waiting ur reply..,
> Yasser
> 
> ObjectType = Image
> NDims = 3
> DimSize = 256 256 28
> ElementType = MET_USHORT
> HeaderSize = -1
> ElementSpacing = 1 1 3
> ElementByteOrderMSB = True
> ElementDataFile = 126_1_%d.img 1 28 1
> 
> --- Lydia Ng <lng at insightful.com> wrote:
> 
> 
>>Yasser,
>>
>>This is a partial solution to what you want. The
>>first step is to be able to
>>read the *.img files as a 3D itk::Image and then the
>>second step is to create
>>the *.dcm files.
>>
>>------------------------------------
>>
>>Each *.img in the IBSR dataset represent one 2D
>>slice (in raw unsigned short
>>format) of a 3D volume.
>>
>>If you want to read them into an ITK image you will
>>have to convert/massage
>>them into a form that ITKIO can handle.
>>
>>The most straightforward thing to do is to create a
>>meta header for it.
>>The meta header is an ascii file. For example, for
>>the 1_24 dataset a meta
>>header would look something like this:
>>--------------------------------
>>
>>ObjectType = Image
>>NDims = 3
>>DimSize = 256 256 65
>>ElementType = MET_USHORT
>>HeaderSize = -1
>>ElementSpacing = 1 1 3
>>ElementByteOrderMSB = True
>>ElementDataFile = 1_24_%d.img -1 63 1
>>
>>------------------------------------------
>>I.e the overall 3D image is (256 x 256) x 65 slices
>>by composing files
>>1_24_-1.img, 1_24_0.img, 1_24_1.img, ... 1_24_63.img
>>
>>The following is a table of starting slice, ending
>>slice and number of total
>>slices you should use for each IBSR dataset if you
>>want it to match up with
>>the corresponding IBSR segmentation file:
>>
>>1_24  -1  63 65 
>>11_3   1  63 63 
>>110_3  0  63 64 
>>111_2  0  63 64 
>>112_2  1  63 63 
>>12_3   1  63 63 
>>13_3   1  63 63 
>>15_3   1  60 60 
>>16_3   1  60 60 
>>17_3   1  63 63 
>>191_3  1  63 63 
>>2_4    1  65 65 
>>202_3  1  63 63 
>>205_3  1  63 63 
>>4_8    7  67 61 
>>5_8    1  60 60 
>>6_10   1  63 63 
>>7_8    1  60 60 
>>8_4    1  63 63 
>>
>>---------------------------------------------
>>Once you got the 3D image into ITK you possibly use
>>the recently checked in 
>>itkGDCMImageIO - I am not familiar with GDCM -
>>perhaps you post a specific
>>question on how to use this IO class.
>>
>>Another (much less elegant) option is to write the
>>image out back out as a
>>.mhd with one contiguous raw image file. I know that
>>Osiris
>>
> 
> (http://www.expasy.org/www/UIN/html1/projects/osiris/osiris.html)
> 
>>let you read in a contiguous raw image file -- you
>>have to fill in a form to
>>to tell it the dimension and spacing -- and it let
>>write it back out as *.dcm
>>(but I don't know how much of the dicom fields are
>>used / filled in).
>>
>>Hope this help,
>>Lydia
>>
>>
>>-----Original Message-----
>>From: yasser salman [mailto:yass71 at yahoo.com] 
>>Sent: Wednesday, June 30, 2004 3:58 AM
>>To: insight-users at itk.org
>>Subject: [Insight-users] IBSR Data
>>
>>hi luis 
>>can i found any software converting *.img to dicom
>>images
>>thanx..,yasser
>>
>>
>>_______________________________________________
>>Insight-users mailing list
>>Insight-users at itk.org
>>http://www.itk.org/mailman/listinfo/insight-users
>>
> 
> 
> 
> 
> 		
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