Dicom image processing and saving

fiji
imagej
segmentation
thresholding
saveimages

#1

Hello evrybody,

would you please guide me?

I have a lot of dicom images and did some processing with matlab but I need to do some process with fiji. I changed my images into 8*bit and did the segmentation but I cannot save it as dicom files (as I need to continue the image processing and building the 3-D skeleton by matlab and …).

Is it possible to segment the images without changing the 16-bit images to 8-bit ones? I am afraid if I lose my data and face problems i building the 3D format of my space!

after processing the images how can I save them as dicom images?As I get several errors after doing the following:
I have downloaded the zipfile “tudordicom_plugin_1.9.30” from the site: (http://santec.tudor.lu/project/dicom/download)

and extracted it and copied the zipfile “TudorDICOM_Plugin” and folder “TudorDICOMLibs” in plugins folder of fiji.

Is there any thing else that I should do?

Thanks a lot,

Esha

P.S. I closed and opened fiji after copying the plugin.


#2

Hello,
Does anyone have any idea how to solve this?
Thanks a lot


#3

Hi @Esha,
so you have processed images in Matlab, segmented them in Fiji and would like to import them back to Matlab?
Is there any specific reason to have them as dicom? Could you try to save them as TIFs and open those TIFs
in Matlab?

Is it possible to segment the images without changing the 16-bit images to 8-bit ones?

It depends, if your 8-bit format gives you enough information (i.e. you are not clipping important parts in shadows or highlights) you can do it. It actually should be even more comfortable because it is twice faster to work with 8-bit images and they occupy twice less memory.

Best regards,
Ilya


#4

we have a dicom writer in petctviewer.org
Add the “pet-ct” update site
And in File-> Save you should see “myDicom” to generate dicom from a stack image

To be stored your stack needs to include a proper dicom header of course (if it is just a mask you want to save just copy the original stack info)