Re: MRI: Plugins, Tips and Data

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Re: MRI: Plugins, Tips and Data

Jonathan Jackson-2
I'm also a graduate student doing mostly MRI post-processing and imagej has
largely become my workhorse.  The plugins I use the most are
   Analyze Reader / Writer
   Plugins listed under "Stacks" - concatenate, remove slices etc
   Process -> Enhance Contrast (use stack) to set display levels
   Volume Viewer or Tony Parker's plugins to view orthogonal slices
   Window Closer (very useful!)
   YAWI 3D plugin for auto contouring
Image comparison
   HyperVolume Browser  (create 4D stack with 2 sliders)
   Process -> Image Calculator (difference images etc)
   Sync Window plugin
   Image->Adjust Threshold and process->Binary

Any numerical processing of images is possible with ImageJ (for an
experienced java programmer, writing custom plugins would not be a big
deal). I don't think ImageJ is a suitable tool for fMRI processing because
there are plenty of other tools specifically for that, but for image
comparison , colour overlay, feature extraction, masking and linear
transformations, imagej is a good bet.

I haven't come across any real 3D mri data on the web.  What kind of thing
were you looking for? - If there is anything that we have that I can
ethically pass on to you I'm happy to do that.


>I am a graduate student interested in MRI post-processing.  I am new
>both to this area and ImageJ, but am an experienced Java programmer.  I
>am wondering:
>1) What kinds of MRI processing have people done with ImageJ, and what
>kinds of things are possible?
>2) What plugins might I need/try?
>3) Where might I find some sample MRI data?

>Any info, tips or links would be appreciated.