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How to see all the values of all the voxels within ROI

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How to see all the values of all the voxels within ROI

Postby stepan_vodopianov » Thu Apr 11, 2019 9:00 am

Good day. I work with MRI image stacks of tumor bearing mice before and after Fe3O4 nanoparticles intravenous injection.
I see some accumulation of negative signal 1h post injection. My goal is to describe this accumulation in details. My idea is to collect the values of the voxels within ROI of tumor before and after and then to compare them.
The comparison of means is not ok - because each time the MRI machine adjusts it's parameters to the mouse position and so on. That's why I am looking for ways to describe what I see - dark spots somewhere inside the tumor 1h post injection - but in mathematical way also - using main principal components analysis or something else.
By the way - I would greatly appreciate for any piece of advice concerning accurate CNR calculation, especially in dynamics using MRI t2 images.

Thanks you in advance,
Posts: 1
Joined: Thu Apr 11, 2019 8:47 am

Re: How to see all the values of all the voxels within ROI

Postby jlancaster » Mon Apr 15, 2019 8:55 am


I'm assuming that you are using the same TR and TE for the pre and post imaging. The problem with the MRI system adjusting scaling might be handled by inspecting the image header and comparing the scaling so that you can adjust both to the same using software such as Mango. The mean values could then be compared, but you might also want to compare the standard deviations, since these relate to the homogeneity of signals in your regions of interest.

Regarding calculation of T2 from multi-echo images, again they would need to be corrected to the same scale factors, by inspecting the headers. Our MRI systems do not scale multi-echo images to different scale factors so they are easier to work with.

I hope this is helpful.

Jack Lancaser
Posts: 4
Joined: Tue Jun 12, 2012 11:16 am

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