Problem using Tudor DICOM plugin in a sequence of pictures

bio-formats
dicom
Tags: #<Tag:0x00007fa30c5f6368> #<Tag:0x00007fa30c5f5800>

#1

Hi. I’m starting to use ImageJ and I’m having some trouble to create a stack of pictures that I made from 940 slices of a brain. The slice thickness is 50 um and I know that my pixel dimensions are 46.5x46.5 um. I need to create a sequence in DICOM format in order to segment some structures in this brain region. I’ve set the scale but my files are not recognized in DICOM viewers. Can you help me with this?


Image analysis and denoise
#2

Hi @acro,

Welcome to the forum.

For importing a series of 2d images, use File > Import > Image sequence...
Then you can set the metadata (pixel spacing) with Image > Properties.

See this page for other information on ImageJ’s DICOM support, including how to export.

Good luck,
John


#3

Hi John
Thank you for your advice but I’ve already done all those steps. I’ve imported the 940 images in 4 steps in order to not overload my RAM and I’ve created 4 stacks. Then I went to Image>Properties and changed the Pixel width and height to 0.0453679 and Voxel depth to 0.05 with my unit of leght in mm and I’ve cliked in Global to replicate to all images. Then I went to Images>Stack>Tools>Concatenate to have one sigle Stack with 940 images.

The problem seems to be in creating DICOM files. I’ve used the Tudor Plugin but it doesn’t work very well. If I instead save my stack in Amira format with the Plugin>Amira>Amira Writer and then use DICOM save function inside Amira it Works. I would love to loose this step because I don’t want to use one more software in my pipeline.

Thank you ver much
Alexandre


#4

Hi @acro,
Thanks for following up. So its an issue with the DICOM writer then…

I don’t know much about the Tudor plugin, but maybe you could explain in more detail what happens when you try to use it. Do other programs open the images but incorrectly? Or do they just fail when trying to open the images written by Tudor? If there is an error message, what does it say. etc…

John


#5

Also, perhaps consider changing the title of this post to something like:
“Problems with Tudor DICOM plugin” or something similar, since that’s the core issue
(I was confused by that before, as you noticed)


#6

I was not sure that I was doing the correct sequence of commands, but your reply was very useful. I also realised now that the problem is probably in Tudor Plugin or in my stack.

I’m going to edit the title.

Thank you very much