Different stacks from MRI

Hi everyone. I’ve got different stacks of MRI images, taken from different point of views. How can i merge those stacks in order to have a 3d rendering of the whole head?
Plus, can I use those stack to get an interface similar to the “orthogonal view” one (that interface uses only one stack, so just one point of view)?
Thanks in advance

I wish I knew a good answer to this question. The 3D Viewer supports rigid landmark registration of multiple 3D volumes, but I could not get it working in a quick test. Your problem is very similar (at least superficially) to the registration problem posed by SPIM/lightsheet microscope data, which is a very hot modality right now—maybe @tpietzsch or @StephanPreibisch have some suggestions here? Is this possible using ClearVolume + BigDataViewer?

In BigDataViewer you can manually align different sources.
Press “T” to start manual transformation. Only the current source (respectively group) is transformed. Press “T” again to fix the transformation relative to the other sources. Press “ESC” to abort.
You can save a settings.xml file for your dataset that persists the manual transformation and is automatically loaded when you open your dataset again.
For more information about getting your dataset into BDV format, see http://imagej.net/BigDataViewer#Exporting_Datasets_for_the_BigDataViewer
The easiest way is probably to pretend it’s a SPIM dataset and do the steps “Dataset Definition” and “Resave the dataset as HDF5/TIFF” from http://imagej.net/Multiview-Reconstruction#Detailed_Tutorials.
Perhaps the Multiview Reconstruction plugin can even register the MRI views for you.

Also, have a look at http://imagej.net/BigWarp which does manual, interactive, landmark-based deformable image alignment and might also be exactly what you need.

Hope that helps…

best regards,
Tobias

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