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software_listing [2017/03/20 13:11] csteel |
software_listing [2018/01/30 14:34] (current) xteng |
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==== Software Listing ==== | ==== Software Listing ==== | ||
+ | |||
+ | === researchers list === | ||
+ | |||
+ | * Anaconda v4.2 for Python 2.7 (https://www.continuum.io/downloads) | ||
+ | * AFNI | ||
+ | * ANTs (http://stnava.github.io/ANTs/) | ||
+ | * BEaST | ||
+ | * BigBrain on line (https://bigbrain.loris.ca/main.php) | ||
+ | * BrainSuite16a1 (http://brainsuite.org/) | ||
+ | * BrainView | ||
+ | * Caret | ||
+ | * CIVET | ||
+ | * Display | ||
+ | * Deformation fields (mcvaneede) | ||
+ | * Eigen v3.2 stable (http://eigen.tuxfamily.org/index.php?title=Main_Page) | ||
+ | * FSL5.0 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) | ||
+ | * FreeSurfer v5.3 (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) | ||
+ | * HCP Workbench (https://www.humanconnectome.org/software/get-connectome-workbench.html) | ||
+ | * MATLAB Compiler Runtime R2015b (https://www.mathworks.com/products/compiler/mcr/) | ||
+ | * Matlab based imaging tools | ||
+ | * brainstorm3[[https://github.com/brainstorm-tools/brainstorm3]] | ||
+ | * eeglab [[https://sccn.ucsd.edu/wiki/How_to_download_EEGLAB]] | ||
+ | * fmristat [[http://www.math.mcgill.ca/keith/fmristat/]] | ||
+ | * surfstat [[http://www.math.mcgill.ca/keith/surfstat/]] | ||
+ | * niak ( https://www.nitrc.org/projects/niak/ ) | ||
+ | * spm8 [[http://www.fil.ion.ucl.ac.uk/spm/software/spm8/]] | ||
+ | * spm12 [[http://www.fil.ion.ucl.ac.uk/spm/software/spm12/]] | ||
+ | * MINC 1 + 2 | ||
+ | * Minc Tools / Display | ||
+ | * pymin | ||
+ | * MRICron tools (http://people.cas.sc.edu/rorden/mricron/install.html) | ||
+ | * mri tutorials | ||
+ | * Mrtrix3 (http://mrtrix.readthedocs.io/en/latest/installation/linux_install.html) | ||
+ | * neurosynth [[https://pkgs.org/download/python-neurosynth]] | ||
+ | * openmp | ||
+ | * RMINC [[https://github.com/Mouse-Imaging-Centre/RMINC]] | ||
+ | * SPM [[https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux]] | ||
+ | * JEMRIS (http://www.jemris.org/) | ||
+ | |||
+ | === Neurodebian Packages === | ||
+ | |||
+ | * FSL | ||
+ | * AFNI | ||
+ | * pyMVPA | ||
+ | * nibabel | ||
+ | * mricron | ||
+ | * psychtoolbox | ||
+ | * odds and ends, converters, viewers and so on. | ||
+ | |||
+ | |||
+ | === Utilities === | ||
+ | |||
+ | * apticron | ||
+ | * Anaconda, miniconda and conda | ||
+ | * FileZilla (https://filezilla-project.org/) | ||
+ | * ethtool | ||
+ | * GCC version to 4.8 if possible (https://gcc.gnu.org/gcc-4.8/) | ||
+ | * GIMP | ||
+ | * InkScape | ||
+ | * OpenOffice | ||
+ | * Perl | ||
+ | * Python | ||
+ | * cffi | ||
+ | * cryptography | ||
+ | * cython | ||
+ | * enum34 | ||
+ | * idna | ||
+ | * imagemagic | ||
+ | * ipaddress | ||
+ | * numpy | ||
+ | * pip | ||
+ | * pyasn1 | ||
+ | * pycosat | ||
+ | * pycparser | ||
+ | * pycrypto | ||
+ | * pygobject | ||
+ | * pyminc | ||
+ | * pyOpenSSL | ||
+ | * python-apt | ||
+ | * scipy | ||
+ | * scour | ||
+ | * six | ||
+ | * unity-lens-photos | ||
+ | * R | ||
+ | * Rminc | ||
+ | * Slack | ||
+ | * SublimeText | ||
+ | * SurfStat | ||
+ | * unattended-upgrades | ||
+ | * Vim | ||
+ | * VirtualBox | ||
+ | * zlib (http://www.zlib.net/) | ||
+ | |||
+ | === BrainVISA Anatomist === | ||
+ | |||
+ | This software has not been tested by our IT Team. Feedback from our research team on this software would be appreciated. | ||
+ | |||
+ | == Description == | ||
+ | |||
+ | BrainVISA Anatomist is a Neuroimaging software platform for mass data analysis | ||
+ | |||
+ | * Morphologist: brain segmentation and sulcal morphometry | ||
+ | * Processing tools and toolboxes | ||
+ | * Interactive 3D neuroimaging data visualization | ||
+ | * Software and data organization | ||
+ | |||
+ | == Resources == | ||
+ | |||
+ | * [[http://brainvisa.info/web/index.html | BrainVISA Homepage ]] | ||
+ | * [[http://brainvisa.info/web/download.html | BrainVISA Downloads]] | ||
+ | * [[http://brainvisa.info/web/download/go.php?url=http://brainvisa.info/packages/4.5.0/linux64-glibc-2.15/brainvisa-installer/brainvisa_installer-4.5.0-linux64-glibc-2.15-online.md5 | BrainVISA md5sums]] | ||
=== MINC Tool Kit === | === MINC Tool Kit === | ||
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* [[https://en.wikibooks.org/wiki/MINC]] | * [[https://en.wikibooks.org/wiki/MINC]] | ||
- | - Minc viewers such as Display, Register, BrainView, ModelGui (Andrew Reid's) | + | - Minc viewers such as: |
+ | * Display | ||
+ | * Register | ||
+ | * BrainView [[https://github.com/sghanavati/brain-view2]] | ||
+ | * ModelGui (Andrew Reid's) | ||
=== SGE === | === SGE === | ||
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=== Development, Programming and Scripting === | === Development, Programming and Scripting === | ||
+ | * adacity | ||
+ | * build-essential | ||
* C | * C | ||
+ | * cmake | ||
+ | * filezilla | ||
* GNC Make | * GNC Make | ||
+ | * gparted | ||
+ | * latex | ||
+ | * pbzip, pigz, rar, p7zip-full | ||
+ | * pdftk, qpdf | ||
* Perl | * Perl | ||
* Python | * Python | ||
+ | * imagemagick | ||
* R | * R | ||
+ | * renameutils | ||
+ | * scribus | ||
+ | * sox | ||
+ | * sshfs | ||
+ | * tree | ||
+ | * vim | ||
+ | * Virtualbox | ||
+ | * watch | ||
=== RMINC === | === RMINC === | ||
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* [[http://www.itksnap.org/pmwiki/pmwiki.php|itk-SNAP]] | * [[http://www.itksnap.org/pmwiki/pmwiki.php|itk-SNAP]] | ||
+ | * [[http://www.itksnap.org/pmwiki/pmwiki.php?n=SourceCode.SourceCode]] | ||
=== Human Connectome Project (HCP) connectome workbench === | === Human Connectome Project (HCP) connectome workbench === |