Posted by
Michael Schmid on
Mar 19, 2010; 10:53am
URL: http://imagej.273.s1.nabble.com/CT-images-negative-intensity-values-Stack-tp3688909p3688911.html
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>
> **********************************************************************
> **
>
>
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