Convert montage with ROIs to stack

[gckujoth]

Hello,

I have montages of MRI images with a large number of ROIs created for
specific white matter structures and I have used these for measurements
in ImageJ. I created the ROIs on the montage image because I found it
helpful to be able to see multiple slices to improve slice-to-slice
consistency in delineating a given structure.

I now wish to convert the montage file with its ROIs to an image stack
that also has the ROIs. (Ultimately, I wish to use the same ROIs
imported into other software for additional analyses and that software
will need to use the image stack.)

Is it possible to translate/convert the ROI coordinates from the montage
to their proper slice positions in the stacked image?

I can easily make an image stack from the montage but the ROIs don't
come along. I also tried to make overlays from the ROIs but these too
fail to survive the conversion of montage to stack. I know I can
flatten/draw the ROIs onto the montage panels before making the stack;
that gives me a stack file with the ROI locations annotated but the ROIs
are not editable.

I'm hoping that I don't have to recreate all the ROIs on the image stacks.

Thanks for any help that anyone can provide.

Greg

--
Gregory Kujoth, Ph.D.
Assistant Scientist
Department of Neurological Surgery
University of Wisconsin

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael Schmid]

Hi Greg,

if you want to keep the ROIs in "Montage to Stack", you could first create a mask, then run "Montage to Stack" also on the stack, and then create selections with "Analyze Particles", adding them to the ROI Manager. You can use the selections of the ROI manager also for the stack of your original image.

The following macro assumes that your original montage is named "Montage" and has 6x6 images. There must be no image named "Mask" at the time when you start the macro.

run("Create Mask");
selectWindow("Montage");
run("Montage to Stack...", "images_per_row=6 images_per_column=6 border=0");
selectWindow("Mask");
run("Montage to Stack...", "images_per_row=6 images_per_column=6 border=0");
rename("StackOfMasks");
run("Analyze Particles...", "  add stack");
selectWindow("Stack");

A limitation of this approach: all rois will become traced rois, thus their accuracy will be limited to pixels (some other rois, e.g. elliptical rois can have subpixel resolution; this will be lost, and ImageJ won't know that it's an elliptical roi any more, so you can't modify it by dragging the corners).

Michael
________________________________________________________________
On Jul 31, 2014, at 05:02, Gregory Kujoth wrote:

> Hello,
>
> I have montages of MRI images with a large number of ROIs created for specific white matter structures and I have used these for measurements in ImageJ. I created the ROIs on the montage image because I found it helpful to be able to see multiple slices to improve slice-to-slice consistency in delineating a given structure.
>
> I now wish to convert the montage file with its ROIs to an image stack that also has the ROIs. (Ultimately, I wish to use the same ROIs imported into other software for additional analyses and that software will need to use the image stack.)
>
> Is it possible to translate/convert the ROI coordinates from the montage to their proper slice positions in the stacked image?
>
> I can easily make an image stack from the montage but the ROIs don't come along. I also tried to make overlays from the ROIs but these too fail to survive the conversion of montage to stack. I know I can flatten/draw the ROIs onto the montage panels before making the stack; that gives me a stack file with the ROI locations annotated but the ROIs are not editable.
>
> I'm hoping that I don't have to recreate all the ROIs on the image stacks.
>
> Thanks for any help that anyone can provide.
>
> Greg
>
> --
> Gregory Kujoth, Ph.D.
> Assistant Scientist
> Department of Neurological Surgery
> University of Wisconsin

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html