Image segmentation (MABS) guidebook

MABS (Multi Atlas Based Segmentation) is a flexible system for performing automatic segmentation of medical images. This guidebook explains how to prepare an atlas for segmentation, how to perform a segmentation, and how to tune MABS for optimal accuracy.

So far, MABS has only been tested on linux, but it probably can work on other platforms. Please contact the email list if you desire to run MABS on other platforms.

Step 1: Creating a master configuration file

First, you should create a new directory for holding your configuration files and training data. You can start with the following layout:

--+------- mabs/
  +------- mabs/task01.cfg

In this context, “task01” refers to a segmentation task with an associated atlas. You can have multiple tasks, such as one task for head and neck, one for prostate, and so on. You don’t have to call it “task01”, you can call it anything. The file “mabs/task01.cfg” is a master configuration file that controls MABS for task01. For purposes of the guidebook, we will use the configuration file specified below:

[TRAINING]
atlas_dir=task01-atlas
convert_dir=task01-convert
prealign_dir=task01-prealign
training_dir=task01

rho_values=0.75:0.25:1.25
sigma_values=L 0.75:0.25:1.5
minimum_similarity=L -0.7:0.2:-0.3
threshold_values=0.2:0.1:0.5

[REGISTRATION]
registration_config=task01-reg

[STRUCTURES]
brainstem
right_parotid
left_parotid

The meaning of each of these parameters will be described as we proceed through the guidebook.

Step 2: Preparing the atlas data

If your input is in DICOM format, you should organize your data like this:

--+------- mabs/
  +------- mabs/task01.cfg
  +---+--- mabs/task01-atlas/
  |   +--- mabs/task01-atlas/subject-01
  |   +--- mabs/task01-atlas/subject-02
  |   +--- mabs/task01-atlas/subject-03

The directory “mabs/task01-atlas” contains the atlas data, and each subject must be placed in a separate subdirectory, but you can name the directories whatever you like. Each subject subdirectory should contain one image (in DICOM format), and one structure set (in DICOM-RT format).

Next, the atlas data should be converted from DICOM-RT into nrrd format using the following command:

plastimatch mabs --convert task01.cfg

After this command completes, you will see newly created directories, containing converted images and structures. The layout is as follows:

--+------- mabs/
  +------- mabs/task01.cfg
  +--+---- mabs/task01-atlas/
  |  +---- mabs/task01-atlas/subject-01
  |  +---- ...
  |  +---- mabs/task01-convert/
  |  +--+- mabs/task01-convert/subject-01/img.nrrd
  |     +- mabs/task01-convert/subject-01/structures/brainstem.nrrd
  |     +- mabs/task01-convert/subject-01/structures/right_parotid.nrrd
  |     +- ...

Finally, you must create a prealign directory. At this time, the prealignment procedure is still under development, so you may simply rename or copy the converted data directory. Here is how to do this on linux:

mv task01-convert task01-prealign

If your input data is not DICOM, you must manually convert them into nrrd, and then put them into the prealign directory as described above.

Step 3: Choose a registration strategy

Next, you must choose a registration strategy for your atlas-based segmentation task. Create the directory “task01-reg”, as specified in the “registration_config” line of the master config file. Within that directory, create one or more registration configuration files. For example:

--+------- mabs/
  +--+---- mabs/task01-reg/
  |  +---- mabs/task01-reg/reg01.txt
  |  +---- mabs/task01-reg/reg02.txt

During the registration optimization phase, each registration configuration file will evaluated against the atlas image. The optimal strategy will be chosen to maximize the Average Dice score over structures defined in the master configuration file.

The format of the registration configuration files follows the format specified in the Image registration guidebook and the Image registration command file reference. However, a GLOBAL section is not needed, nor should one be specified. The following example is a bare-bones configuration:

# == reg01.txt ==
# A single B-spline stage, with 10 cm grid spacing
[STAGE]
xform=bspline
impl=plastimatch
grid_spac=100 100 100
regularization_lambda=10
max_its=30
res=4 4 2

Here is another, more complicated example, which may or may not give better results:

# == reg02.txt ==
# First, truncate HU values to range [-1000,1000]
[PROCESS]
action=adjust
parms=-inf,0,-1000,-1000,1000,1000,inf,0
images=fixed,moving

# Next, do a grid search to find good global translation
[STAGE]
xform=translation
impl=plastimatch
gridsearch_min_overlap=0.8 0.8 0.8
res=4 4 2

# Next, do a local search to improve translation
[STAGE]
xform=translation
impl=itk
optim=rsg
res=4 4 2

# Finally, a single B-spline stage, with 10 cm grid spacing
[STAGE]
xform=bspline
impl=plastimatch
grid_spac=100 100 100
regularization_lambda=10
max_its=30
res=4 4 2

Once you have created one or more registration parameter file, you can run a training routine to evaluate them, as follows:

plastimatch mabs --train-registration task01.cfg

This will take a long time to run. If you have a large atlas and you want to evaluate several strategies, it may run for several days. In the end, you will get a directory layout which looks like this:

--+----------- mabs/
  +--+-------- mabs/task01/
  +--+--+----- mabs/task01/mabs-train/
  +--+--+--+-- mabs/task01/mabs-train/subject-01/...
  +--+--+--+-- mabs/task01/mabs-train/subject-02/...

The “mabs-train” directory contains results from exhaustive testing of all pairs of atlas members on all registration strategies. These results are analyzed by running a script in the plastimatch source code directory:

plastimatch-source/extra/perl/digest_mabs_stats.pl --save-optimization-result task01/mabs-train

You will see something like this:

reg: reg01.txt,0.498976166666667,8.938063
reg: reg02.txt,0.673245246153846,5.02114200090498

Which means that the first registration strategy (reg01.txt) had an average Dice of 0.49 and an average 95-boundary Hausdorff of 8.9. The second strategy (reg02.txt) was better, and therefore was selected. The script writes another file which confirms this choice to MABS.:

--+----------- mabs/
  +--+-------- mabs/task01/
  +--+--+----- mabs/task01/mabs-train/
  +--+--+----- mabs/task01/mabs-train/optimization_result_reg.txt

Step 4: Choose a segmentation strategy

Next, you must optimize the voting parameters. This is easier than optimizing the registration strategy, because there are a fixed set of parameters to be optimized. The search range is specified in the master configuration file, for example, like this:

rho_values=0.75:0.25:1.25
sigma_values=L 0.75:0.25:1.5
minimum_similarity=L -0.7:0.2:-0.3
threshold_values=0.2:0.1:0.5

To run the segmentation optimization, do this:

plastimatch mabs --train task01.cfg

This will also take a long time to run. If you have a large atlas, it may run for several days. In the end, you will get additional files and directories like this:

--+----------- mabs/
  +----------- mabs/seg_dice.csv
  +--+-------- mabs/task01/mabs-train/subject-01/segmentations/...

Once again, run the analysis script:

plastimatch-source/extra/perl/digest_mabs_stats.pl --save-optimization-result task01/mabs-train

Which should give something like this:

reg: reg01.txt,0.498976166666667,8.938063
reg: reg02.txt,0.673245246153846,5.02114200090498
seg (dice): BrainStem,1.250000,31.622776,0.199526,0.200000,0.8218795
seg (hd95): BrainStem,1.250000,5.623413,0.316228,0.200000,2.468004
seg (dice): Parotid_L,1.000000,31.622776,0.199526,0.300000,0.71477
seg (hd95): Parotid_L,1.000000,31.622776,0.199526,0.500000,3.544994

This tells you the optimal segmentation parameters for each structure. For example, using the dice criteria, the optimal values for the BrainStem structure are rho=1.25, sigma=31.6, minsim=0.20, and thresh=0.20. The average Dice of the BrainStem using these parameters is 0.82. The script writes yet another file which tells mabs which parameter values are optimal according to the Dice metric.:

--+----------- mabs/
  +--+--+----- mabs/task01/mabs-train/optimization_result_seg.txt

Step 5: Running a segmentation

Whew! That was a lot of work. But now you are ready to run segmentations. If your images are in directory “input-dicom”, you can do this:

plastimatch mabs --segment dicom-in --output result-directory task01.cfg

This will segment the input image, and create an output directory which contains the segmented structures (and a lot of other files too).