(Ubuntu14.04) How to install mipav7.2 and it’s plugins (e.g., TOADS-CRUISE) correctly (Ubuntu)

mipav is a powerful imaging tool developed by NIH (http://mipav.cit.nih.gov/), providing a lot of help in medical imaging analysis, such as registration, level set, segmentation, etc.

When I came across installing mipav(+plugins), I got a lot of problems. Installing mipav itself does not cause problem, the problem is that if you don’t install mipav correctly, you will get a lot of troubles in installing plugin (i.e., cannot install the plugin even though the plugin has no problems). Here it’s the brief flow.

1. Install mipav (from http://mipav.cit.nih.gov/).

sh ./installMIPAV.bin

NOTE: if you do sudo, your files will be installed in the root/ instead

2. Just follow ALL the default setting (i.e., where is the mipav/ folder is, where is the plugin folder is). If you choose the location, it’s fine for mipav running, but you will soon find out it cause problems in installing plugin. For example, the plugin folder will STILL placed in the ~/mipav/plugins. (For the shortcut, it’s fine)

3. Assume you are at ~. Open mipav and make sure there are no error messages. (WARNINGL mipav is very sensitive to if you are using sudo or not. If you don’t install with sudo, then you should just do ./MIPAV. Otherweise, the plugins folder will be automatically put into root, which is confusing)

>> ./MIPAV

4. Install JIST before TOADS-CRUISE). Follow this: https://masi.vuse.vanderbilt.edu/images/8/82/TR-MASI-10-01.pdf

HOWEVER, please note:

– After you download JIST in any folder and use mipav to install it, it will most likely show you error message: ” No plugins were installed, please select valid MIPAV plugin files”.  This error message is misleading. When you go to the mipav/plugins, you will find the the folder is not empty and in fact when you open mipav, you will see under “Plugins” in the menu, you plugin is installed.

(NOTE: Sometime, you will find nothing in the plugin folder. After trial and errors, I find the solution: PUT YOUR jar FILE INTO THE PLUGIN FOLDER INsIDE MIPAV/. And then install the plguin from there. I think the problem is that for some reasons mipav is not able to find the decompressed files during installation. )

5. Then install TOADS-CRUISE following this: https://masi.vuse.vanderbilt.edu/images/8/82/TR-MASI-10-01.pdf

6. You are good to go.

(Please contact me if you have any questions: johnny5550822@gmail.com) Good luck!

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Notes about imaging tool FSL

FSL is a famous tool for medical imaging analysis. Here are some notes.

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/

(Note: Assume you are using ubuntu, and you use Debian repo to install fsl, which all the fsl softwares started with fsl5.0-“)

1. To open the FSL in terminal, type “fsl5.0-fsl”.

2. FSL only can view nii images, use dcm2nii to convert DICOM to nii.

(use software center to install dcm2nii)

3. Use FLIRT linear registration for image registration

4. 4D nii is a stack of 3D nii  files along time (time-series data).

5. fsl5.0-flirt for 3D registration (fsl5.0-mcflirt for 4D registration)

6. Do Skull removal before brain registration.

7. Choose image with higher resolution as reference