[Insight-users] IBSR Data

[yasser salman]

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
> 
> 
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> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
> 



		
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