General Analysis Software
The below table lists some of the 3rd party analysis software available at the center. In most cases to use the software you would just add the given path (or that path with “/bin” or version # or both appended — take a look at what is in the path) to your shell PATH to use the software. Or run using the full path to the binary.
| Software Name | Last Updated | NMR Path | Maintainer | Instructions |
|---|---|---|---|---|
| AFNI | 5/22/2023 | /usr/pubsw/packages/AFNI | help@nmr | Installed version 23.1.05 |
| ANTs | 1/21/2020 | /usr/pubsw/packages/ANTS | help@nmr | Installed version 2.3.4 |
| ATPP_GUI | 6/7/2017 | /usr/pubsw/packages/ATPP | help@nmr | Installed version 2.1.0 |
| BART Toolbox | 10/17/2017 | /usr/pubsw/packages/bart | help@nmr | Installed version 0.4.01 |
| BASIL | 4/11/18 | /usr/pubsw/packages/oxford_asl | help@nmr | /usr/pubsw/packages/oxford_asl/README.txt |
| Caffe | 11/25/2015 | /usr/pubsw/packages/caffe | help@nmr | |
| DicomBrowser | 10/21/2015 | /usr/pubsw/bin/dicombrowser | gwarner | |
| Docker | On select machines upon request | help@nmr | Docker @ Martinos | |
| DSI Studio | 9/3/2021 | /usr/pubsw/packages/DSI-Studio | help@nmr | |
| fMRIPrep | 10/10/2023 | /usr/pubsw/packages/fmriprep/ | help@nmr | Built Singularity version 23.1.4 |
| Freesurfer | weekly | /usr/local/freesurfer | fsdev | http://www.freesurfer.net/fswiki/InternalFreeSurferDistributions |
| FSL | 12/30/2020 | /usr/pubsw/packages/fsl | help@nmr | https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/ShellSetup |
| FSLeyes | 1/7/2019 | /usr/pubsw/packages/FSLeyes | help@nmr | Installed version 0.27.0 |
| heudiconv | 2/27/2020 | /usr/pubsw/packages/heudiconv | help@nmr | Latest Singularity build is heudiconv_0.8.0.sif |
| ITK | 10/30/2014 | /usr/pubsw/packages/itk | http://itk.org/ITK/resources/resources.html | |
| Mathematica | 7/20/15 | /usr/pubsw/bin/mathematica | help@nmr | |
| Matlab | 4/10/2018 | /usr/pubsw/bin/matlab (/cluster/matlab) | help@nmr | |
| Mendeley | 6/5/2018 | /usr/pubsw/bin/mendeleydesktop | help@nmr | Installed version 1.19 |
| MRIcron | 3/19/2015 | /usr/pubsw/packages/MRIcron | ||
| MRtrix3 | 5/11/2023 | /usr/pubsw/packages/mrtrix | help@nmr | |
| occiput | 7/9/2015 | /usr/pubsw/packages/occiput | occiput@nmr | |
| picasso | 10/27/16 | /usr/pubsw/packages/picasso | ||
| PPI Toolbox | 4/11/2014 | /usr/pubsw/common/spm/spm8/toolbox/PPPI/ | mclaren | |
| Python | see list | /usr/pubsw/packages/python | martinos-python | http://freesurfer.net/fswiki/DevelopersGuide/NMRCenterPython/UsersGuide |
| R | 3/12/2024 | /usr/pubsw/packages/R | help@nmr | http://r-project.org (latest installed 4.3.3) |
| Singularity | 1/22/2020 | /usr/bin/singularity | help@nmr | Singularity @ Martinos |
| Slicer | 2/25/2019 | /usr/pubsw/packages/slicer/ | help@nmr | http://slicer.org/slicerWiki/index.php/Main_Page |
| SlicerSALT | 8/1/2017 | /usr/pubsw/bin/SlicerSALT | help@nmr | http://salt.slicer.org/docs/ |
| SPM | 2/21/2018 | /usr/pubsw/common/spm | aschultz | Installed version 7219 |
| TORTOISE | 6/28/2017 | /usr/pubsw/packages/TORTOISE | mhibert | Installed version 3.0.0 |
| Workbench | 6/28/2017 | /usr/pubsw/packages/workbench | help@nmr | Installed version 1.2.3 |
| vtk | /usr/pubsw/packages/vtk | fsdev |
You can see many other packages if you just do “ls /usr/pubsw/packages” but if not listed above they are even less likely to be well maintained.
We will give “best effort” to make a general install of most packages requested. In general we do not proactively update till someone asks for a new version. Also many packages are maintained by volunteers or, as in the case of Freesurfer, the actual developers. MATLAB, R, AFNI and FSL are the packages the IT support group is most on top of.
Please note you cannot install OS packages (RPM/apt-get/YUM/dpkg/…) as a non-root user. However most of these tools have GITHUB repos that let you build them in your own lab directories. Building can very from trivial to near impossible depending on what other package/library dependecies they have. And a lot of tools also are installable using your own Python Anaconda distribution.
If the package distributes a *.zip file or something called a tarball (*.tar.gz or *.tgz) those can usually be extracted using ‘unzip’ or ‘tar’ command to your own lab directories to run from there too. However, depending on where the binaries were built they may not run on our CentOS/Rocky systems and need to be built from code. This is most likely the case if you get unfound shared library errors.
