software_listing

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software_listing [2017/04/03 13:28] – csteelsoftware_listing [2024/03/26 13:52] (current) – external edit 127.0.0.1
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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 === === BrainVISA Anatomist ===
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 == Resources == == Resources ==
  
-  * [[http://brainvisa.info/web/index.html | Homepage ]] +  * [[http://brainvisa.info/web/index.html | BrainVISA Homepage ]] 
-  * [[http://brainvisa.info/web/download.html | Downloads]] +  * [[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 | md5sums]]+  * [[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 ===
  • software_listing.1491226131.txt.gz
  • Last modified: 2024/03/26 13:52
  • (external edit)