ASHS requires the Linux or MacOS operating system. It has been tested most extensively on Centos 6.3, but should work with newer versions of Linux and MacOS. For segmenting many subjects and for generating new atlas packages, we recommend installing ASHS on a Linux cluster running the Sun Grid Engine. In our environment, we run ASHS on a Linux Rocks cluster.
You can also run ASHS on a standalone Linux or MacOS workstation running GNU parallel. On an eight-core machine, a single segmentation will take under 30 minutes.
The easiest way to try out ASHS is to run ASHS on the cloud.
1. 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 for ASHS atlas sets.
2. Uncompress the software package in the directory of your choice
> cd /home/pauly/ashs> unzip ashs-fastashs-20170223.zip3. Set up your Linux environment. Users of the bash shell can add the following code to their .bashrc file:
> export ASHS_ROOT=/home/pauly/ashs/ashs-fastashsUsers of csh shell should add the following line to their .cshrc file:
> setenv ASHS_ROOT /home/pauly/ashs/ashs-fastashs4. Verify the installation. Executing scripts ashs_main.sh and ashs_train.sh with the options -h should print the usage instructions for these commands.
> $ASHS_ROOT/bin/ashs_main.sh -h ashs_main: automatic segmentation of hippocampal subfieldsusage: ashs_main [options]...> $ASHS_ROOT/bin/ashs_train.sh -h...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
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) but some only work with older ASHS versions. We will update these atlases soon. Write us if you need them!
Some users may prefer to build their own atlas package, instead of using one of the packages that we provide. Please see the Building an atlas for T2-MRI or T1-MRI pages for details.
To use an existing atlas package follow these steps.
1. Download the desired atlas package from NITRC to a directory of your choice.
2. Uncompress the atlas package
> cd /home/pauly/ashs/atlases> tar -xvf ashs_atlas_upennpmc_20161128.tar ashs_pmcThe atlas package will be created in a subdirectory ashs_pmc
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 allows you to debug registration problems easily 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.