Albo is a tool for calculating the overlap between a lesion and brain regions, based on MRI sequences. Given a set of MRI images, the lesion is automatically segmented and then registered to a standard brain. Now, the lesion overlap with brain regions is calculated based on brain atlases.

The following programs are needed for installing and running albo:

• NumPy
• SciPy
• Computational Morphometry Toolkit (CMTK)
• FSL
• NiftyReg

Apart from NiftyReg, in Ubuntu these programs can be installed with the command

sudo apt-get install python-numpy python-scipy cmtk fsl

NiftyReg needs to be built from source, see here for instructions.

After installation, you may need to add something like source /etc/fsl/5.0/fsl.sh to your .bashrc file, depending on your FSL version. This makes, e.g., the command bet available, instead of fsl5.0-bet, which is required by albo. See man fsl for details.

Download and unpack the program (or clone the repository) and run python setup.py install. This may download further Python dependencies.

Open the file ./config/albo/albo.conf and set the paths needed by the program. Then, place the classifiers, standardbrains and

This section provides just a rough overview. See the wiki for more information, or run albo -h in your terminal.

Configure the necessary paths in ~/.config/albo/albo.conf.

To list all available classifiers and the sequence identifiers they emply, use

albo list

Assuming there is a classifier identifying the FLAIR sequence as MR_Flair and the T1 sequence as MR_T1, to run the program, use

albo run --id case-id MR_Flair:path/to/flair MR_T1:path/to/t1

In case new atlases were added to the atlas directory, re-calculate the overlap for all previously segmented cases with

albo update