CT images - negative intensity values; Stack

[Ganesh Narayanasamy-2]

Here is a newbie to ImageJ. I have a stack of 2D CT 16-bit images in DICOM format that I am interested in saving in tiff or jpeg format with out the negative intensity pixel values. In order to preserve the image intensity range, Can I just add 1024 to the Hounsfield unit of all the pixels and make the intensities positive?

2nd Query: Since it is time consuming to open each image and saving it individually, I would like to import sequence and save as a single stack of 3D tiff or jpeg image.

When I opened the stack of 2D-CT images in DICOM format using File>Import>ImageSequence, the file stack opened in an incorrect order. Here are the file names (and the order in which it  got opened in ImageSequence within brackets). Notice that file name includes longitudinal position information like 137mm, 139.5mm etc.
CT.rtp1.1.CHESTCT.T.137.CT.dcm (5)
CT.rtp1.1.CHESTCT.T.139.5.CT.dcm (1)
CT.rtp1.1.CHESTCT.T.142.CT.dcm (3)
CT.rtp1.1.CHESTCT.T.144.5.CT.dcm (6)
CT.rtp1.1.CHESTCT.T.147.CT.dcm (4)
CT.rtp1.1.CHESTCT.T.149.5.CT.dcm (2)
 
I would like to open the images in the sequence given above but don't know how to. So, I tried these steps but
in vain.
a) Removed the dots in filename, b) Replaced dots with "_" , c) Appended a number to the end of the filename
like CTrtp11CHESTCTT137CT_1.dcm, CTrtp11CHESTCTT1395CT_2.dcm etc but that did not help either.
 
I tried playing around with options in the Image sequence pop-up menu like Starting Image:1, Increment:1; Sort
Images Numerically etc, that did not work either.Hope someone can clarify.  Thank you,
Ganesh

************************************************************************

"What the mind of man can conceive and believe, It can achieve" - Napolean Hill

-Ganesh
Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center

Earlier work:
http://www.sciencedaily.com/releases/2007/05/070504133017.htm

************************************************************************

     
_________________________________________________________________
Hotmail: Trusted email with powerful SPAM protection.
http://clk.atdmt.com/GBL/go/210850553/direct/01/

[Michael Schmid]

Hi Ganesh,

in 'Import Sequence', sorting is done the following way:
If all file names have the same length, it is simple alphanumeric  
(ascii) sorting.
Otherwise (true in your case), all numeric characters in a file name  
are put together, and the list is sorted by ascending number.

So for your first files:
   CT.rtp1.1.CHESTCT.T.137.CT.dcm   ->  11137
   CT.rtp1.1.CHESTCT.T.139.5.CT.dcm -> 111395
   CT.rtp1.1.CHESTCT.T.142.CT.dcm   ->  11142

So, you need a decimal fraction in all of your filenames, ore in  
none, to make it work.
Maybe you can do the slices at a spacing or 2 instead of 2.5 mm or  
start at 137.1 mm (giving 139.6, 142.1, etc.).
Otherwise you need a macro to rename the files. Here is an idea for  
how to get the new file name:

newFileName = replace(oldFileName, "([0-9][0-9])\\.CT\\.dcm", "$1\\.0\
\.dcm");

Michael
________________________________________________________________

On 18 Mar 2010, at 16:28, Ganesh Narayanasamy wrote:

> Here is a newbie to ImageJ. I have a stack of 2D CT 16-bit images  
> in DICOM format that I am interested in saving in tiff or jpeg  
> format with out the negative intensity pixel values. In order to  
> preserve the image intensity range, Can I just add 1024 to the  
> Hounsfield unit of all the pixels and make the intensities positive?
>
> 2nd Query: Since it is time consuming to open each image and saving  
> it individually, I would like to import sequence and save as a  
> single stack of 3D tiff or jpeg image.
>
> When I opened the stack of 2D-CT images in DICOM format using  
> File>Import>ImageSequence, the file stack opened in an incorrect  
> order. Here are the file names (and the order in which it  got  
> opened in ImageSequence within brackets). Notice that file name  
> includes longitudinal position information like 137mm, 139.5mm etc.
> CT.rtp1.1.CHESTCT.T.137.CT.dcm (5)
> CT.rtp1.1.CHESTCT.T.139.5.CT.dcm (1)
> CT.rtp1.1.CHESTCT.T.142.CT.dcm (3)
> CT.rtp1.1.CHESTCT.T.144.5.CT.dcm (6)
> CT.rtp1.1.CHESTCT.T.147.CT.dcm (4)
> CT.rtp1.1.CHESTCT.T.149.5.CT.dcm (2)
>
> I would like to open the images in the sequence given above but  
> don't know how to. So, I tried these steps but
> in vain.
> a) Removed the dots in filename, b) Replaced dots with "_" , c)  
> Appended a number to the end of the filename
> like CTrtp11CHESTCTT137CT_1.dcm, CTrtp11CHESTCTT1395CT_2.dcm etc  
> but that did not help either.
>
> I tried playing around with options in the Image sequence pop-up  
> menu like Starting Image:1, Increment:1; Sort
> Images Numerically etc, that did not work either.Hope someone can  
> clarify.  Thank you,
> Ganesh
>
> **********************************************************************
> **
>
> "What the mind of man can conceive and believe, It can achieve" -  
> Napolean Hill
>
> -Ganesh
> Narayanasamy,Ph.D., PostDoc-University of Kentucky Cancer Center
>
> Earlier work:
> http://www.sciencedaily.com/releases/2007/05/070504133017.htm
>
> **********************************************************************
> **
>
>    
> _________________________________________________________________
> Hotmail: Trusted email with powerful SPAM protection.
> http://clk.atdmt.com/GBL/go/210850553/direct/01/

[EHB2010]

what range of pixel values is there now? how many bits are the images? Have you looked at the source code for the particular image stack opener you are using to see how it orders the images? BW