You are viewing the documentation for classic ASHS

For new projects we recommend HyperASHS, which produces isotropic-resolution segmentations of the same structures and is available in the cloud through ITK-SNAP as well as locally.

Local ASHS: Installation¶

Requirements¶

ASHS requires the Linux or MacOS operating system. For segmenting many subjects and for generating new atlas packages, we recommend installing ASHS on a Linux cluster running Sun Grid Engine or a compatible scheduler.

You can also run ASHS on a standalone Linux or MacOS workstation using GNU parallel. On an eight-core machine, a single segmentation takes under 30 minutes.

Tip

The easiest way to try out ASHS is to run ASHS on the cloud.

Download and install the ASHS software¶

Download the latest release of the ASHS software package from the NITRC repository. Be sure to download the software itself, under the fast-ashs package. The other packages are ASHS atlas sets.
Uncompress the software package in the directory of your choice:
```
cd /home/pauly/ashs
unzip ashs-fastashs-20170223.zip
```
Set up your environment. Users of the bash shell can add the following line to their .bashrc file:
```
export ASHS_ROOT=/home/pauly/ashs/ashs-fastashs
```
Users of the csh shell should add the following line to their .cshrc file:
```
setenv ASHS_ROOT /home/pauly/ashs/ashs-fastashs
```

Verify the installation. Running the scripts ashs_main.sh and ashs_train.sh with the -h option should print the usage instructions for these commands:

$ $ASHS_ROOT/bin/ashs_main.sh -h
ashs_main: automatic segmentation of hippocampal subfields
usage:
  ashs_main [options]
...
$ $ASHS_ROOT/bin/ashs_train.sh -h
...

Download and install ASHS atlas packages¶

ASHS atlas packages are required to perform segmentation. Different atlas packages are based on different segmentation protocols. Be sure to download an atlas that is compatible with the current version of ASHS (1.0.0 or later). The most commonly used ASHS atlas is:

The ASHS UPENN PMC atlas package (2014 paper), developed in collaboration with Dr. David A. Wolk at the University of Pennsylvania (Penn) Memory Center. It labels subfields along the entire length of the hippocampal formation and includes several cortical regions (PRC/ERC). This atlas package is suitable for labeling older adult brains in 3 Tesla MRI.

Several additional atlases are available (7T older adults, 3T younger adults, 3T older adults hippocampal body only, and 3T older adults for T1-weighted MRI), and are listed on the Models and Atlases page. Some only work with older ASHS versions.

Some users may prefer to build their own atlas package instead of using one of the packages that we provide. See Building an Atlas for T2-MRI or Building an Atlas for T1-MRI for details.

To use an existing atlas package:

Download the desired atlas package from Hugging Face or NITRC to a directory of your choice. See Models and Atlases for the list of packages.
Uncompress the atlas package:
```
cd /home/pauly/ashs/atlases
tar -xvf ashs_atlas_upennpmc_20161128.tar ashs_pmc
```
The atlas package will be created in the subdirectory ashs_pmc.

Download and install ITK-SNAP¶

We recommend also installing ITK-SNAP on the system. ITK-SNAP can be used to view images and segmentation results. If possible, install ITK-SNAP version 3.6.2 or later, which makes it easy to debug registration problems and to perform manual registration when automatic registration fails.

The instructions in this tutorial assume that ITK-SNAP can be invoked from the command line by entering itksnap.

See the equivalent page for HyperASHS.