--- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # Multi Atlas Segmentation and Morphometric Analysis Toolkit (MASMAT) -> Originally designed for mouse brain MRI, but is applicable to any spicious (e.g. Non-human primate, or even human neuroimages) + Originally designed for mouse brain MRI, but is applicable to any spicious (e.g. Non-human primate, or even human neuroimages) Author: Da Ma (dma@wakehealth.edu; da_ma@sfu.ca; d.ma.11@ucl.ac.uk) ## Description -> Automatic brain structural parcellation through registration-based segmentation-propagation and multi-atlas-based label-fusion +Automatic brain structural parcellation through registration-based segmentation-propagation and multi-atlas-based label-fusion This bash scripts is created for `Multi-atlas based automatic brain structural parcellation`, mainly for mouse brain MRI. This script achieve automatic brain MRI image segmentation with given [__mouse brain MRI atlases__](https://github.com/dancebean/mouse-brain-atlas) - which is a set of pairs of template images along with their manually labells. Sample atlases can be downloadable from the Github respsitory [here](https://github.com/dancebean/mouse-brain-atlas). For detailed description of the pipeline, please refer to the papers [[1]](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086576) [[2]](https://www.frontiersin.org/articles/10.3389/fnins.2019.00011). [Citation](#citation) of the two papers are listed at the bottom of this page. @@ -116,7 +116,7 @@ - `-e`: specify to run locally (`local`) on on `cluster` . Specify `cluster` will submit parallel pbs jobs to cluster; specify `local` will run job sequentially on local machine. cluster is set by default = Step 2. bias field correction -> This is an important step before the parcellation. It is skipped in the demo as the images are already "bias-corrected" using the N4 algorithm +This is an important step before the parcellation. It is skipped in the demo as the images are already "bias-corrected" using the N4 algorithm `mas_N4_batch` - Step 3. __*brain structure parcellation*__ @@ -136,8 +136,6 @@ - `-a`: text file list the templates inside the atlas folder to be used (default: `template_list.cfg` file within the atlas folder) - `-p`: configuration file to tune the parameters for the registration and label fusion algorithms -### Sample image of the pipeline output -[ "Click for sample quality control image of the parcellation output (generated using mas_quickcheck)."](docs/quickcheckdemo.png) The similar color between the olfactory bulb and the cortex is due to the limited colormap of `jet`. ## List of functions