Looking for the MAGeT Morphology pipeline? Use the morpho-labelmask
branch instead.
Given a set of labelled MR images (atlases) and unlabelled images (subjects), MAGeT produces a segmentation for each subject using a multi-atlas voting procedure based on a template library made up of images from the subject set.
Here is a schematic comparing 'traditional' multi-atlas segmentation, and MAGeT brain segmentation:
The major difference between algorithms is that, in MAGeT brain, segmentations from each atlas (typically manually delineated) are propogated via image registration to a subset of the subject images (known as the 'template library') before being propogated to each subject image and fused. It is our hypothesis that by propogating labels to a template library, we are able to make use of the neuroanatomical variability of the subjects in order to 'fine tune' each individual subject's segmentation.
To cite MAGeTbrain in publications, please use:
Pipitone J, Park MT, Winterburn J, et al. Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates. Neuroimage. 2014;
M Mallar Chakravarty, Patrick Steadman, Matthijs C van Eede, Rebecca D Calcott, Victoria Gu, Philip Shaw, Armin Raznahan, D Louis Collins, and Jason P Lerch. Performing label-fusion-based segmentation using multiple automatically generated templates. Hum Brain Mapp, 34(10):2635–54, October 2013. (doi:10.1002/hbm.22092)
In order to use MAGeTBrain, you will need to install:
or
Just use the pipeline on Compute Canada's Niagara Cluster.
git clone https://github.com/CobraLab/MAGeTbrain.git
source MAGeTbrain/bin/activate
mb init segmentations
cd segmentations
mb import atlas1_t1.mnc atlas1_labels.mnc
mb import atlas2_t1.mnc atlas2_labels.mnc
...
mb check
mb run
Check out a copy of this repository somewhere handy,
git clone https://github.com/CobraLab/MAGeTbrain.git
Add the MAGeTbrain/bin
folder to your path. This can be done easily by
running, source MAGeTbrain/bin/activate
(revert PATH by typing deactivate
).
Create a new folder for your project and,
mb init
Copy/link your atlases, templates, subjects into input/atlases
,
input/templates
, and input/subjects
, respectively. As per always, MR
images go in brains
.
Atlas labels are expected to have the same name as their MR image but with a
postfix of _labels.mnc
. Use the import
command to simplify the renaming
process:
mb import /path/to/image_file.mnc /path/to/label_file.mnc
This copies the image and label files into the proper folder and rename the
label file accordingly. Use the mb import -l
to use symbolic links rather
than copying files.
MAGeT Brain is operated using the mb
command. In order to run the
entire pipeline, simply run:
mb run
This uses the default settings to execute the necessary commands. In
particular, it assumes you have access to a qbatch-enabled batch queuing system, and
uses the utility qbatch
to submit commands in batches. If you are
running this on Niagara, you should have no problems.
If you can also run MAGeT Brain using the GNU parallel on a single machine, like so:
mb run -q parallel
Currently, only majority voting label fusion is enabled. For a more complete implementation, check the 'master' branch.
mb init
mb init [<folder>]
The init
command is used to start a new project. It creates a folder
structure to hold MAGeT brain inputs and outputs. If no folder name is supplied
then the current folder is used. init
creates the following folders:
project-folder/
input/
atlases/
brains/
labels/
templates/
brains/
subjects/
brains/
output/
mb import
mb import <image.mnc> <labels.mnc> [<mask.mnc>]
The given image and corresponding labels are imported into the input/atlases
folder, with the proper naming convention.
mb check
Checks the input configuration and reports any anomalies and suggestions to correct them. If this command doesn't return any messages then you should be set to run MAGeT brain.
mb status
Reports on the progress of MAGeT brain and shows the number of remaining tasks.
mb run
Starts the MAGeT brain pipeline.
For an in-depth guideline, follow the MAGeTbrain and the MAGeTmorph tutorials.
http://tinysong.com/y9lO