Registration of Bruker MR images


#1

Hi,

I’m new to imagej and I was wondering if anyone has developed a work-flow for the registration of MR images from Bruker instruments. I have tried to do this, but I keep running into a host of errors and am about to give up and try other software.

Laurel


#2

Hello @laurel and welcome to the ImageJ forum!

What type of images are they? 3D? What is the deformation you expect between them and what methods/plugins have you tried so far?


#3

They are 2d 256x256 images with the same number of pixels, field of view, sequence, etc. Images of mouse brains in the head of the living mouse.
I need to slightly rotate, translate and scale X and Y pixels so that one image can be subtracted from the other. For the most part the deformations
are small. Most of the images just need translation and rotation.

I tried the registration in imageJ but I could get nowhere because everything I tried failed. E.g., I tried to put the images read with the Bruker plugin
into a stack, but this failed because imageJ did not like the image parameters, etc.


#4

@laurel, could you post here a couple of your images so we better understand your problem? You can also upload a whole stack somewhere we can access it.


#5

OK, the images are the standard 2dseq files at the end of the Bruker file tree, e.g.,

7d-1NPCinjection/yiyang.20160309.rat.nano17.befinj.Aw1/3/pdata/1/2dseq

In order for ImageJ to read these, it needs the BrukerOpener.jar plugin. I assume that you would need the entire file tree in order to parse the parameters correctly in ImageJ. I tried to upload one of these, but this web site does not allow 2dseq files because they are not tiffs, jpegs, etc.

Perhaps I can put a couple of these into DropBox for you? I tried to copy and paste some images here, but no luck.

I think the first thing to do is to try to make these into some kind of stack?

Each 2dseq file contains several slices from front to back of the mouse head showing the various planes of the brain.


#6

@laurel

Just in case… have you seen this MRI File Manager (Bruker) plugin? It seems to be more-recently developed than BrukerOpener anyway. Might be worth a try as well…

eta