software_listing

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software_listing [2017/06/13 16:48] – csteelsoftware_listing [2024/03/26 13:52] (current) – external edit 127.0.0.1
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 === researchers list === === researchers list ===
  
-- Anaconda v4.2 for Python 2.7 (https://www.continuum.io/downloads) +  * Anaconda v4.2 for Python 2.7 (https://www.continuum.io/downloads) 
-- AFNI ( +  * AFNI 
-- ANTs (http://stnava.github.io/ANTs/) +  * ANTs (http://stnava.github.io/ANTs/) 
-- BrainSuite16a1 (http://brainsuite.org/) +  * BEaST 
-- CIVET +  * BigBrain on line (https://bigbrain.loris.ca/main.php) 
-- Deformation fields +  * BrainSuite16a1 (http://brainsuite.org/) 
-- Eigen v3.2 stable (http://eigen.tuxfamily.org/index.php?title=Main_Page) +  * BrainView 
-- FSL5.0 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) +  * Caret 
-- FreeSurfer v5.3 (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) +  * CIVET 
-- HCP Workbench (https://www.humanconnectome.org/software/get-connectome-workbench.html) +  * Display 
-- MATLAB Compiler Runtime R2015b (https://www.mathworks.com/products/compiler/mcr/) +  * Deformation fields (mcvaneede) 
-- Minc Tools / Display +  * Eigen v3.2 stable (http://eigen.tuxfamily.org/index.php?title=Main_Page) 
-- Mricron tools (http://people.cas.sc.edu/rorden/mricron/install.html) +  * FSL5.0 (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) 
-- Mrtrix3 (http://mrtrix.readthedocs.io/en/latest/installation/linux_install.html)+  * 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 ===
  
-=== Utilities+  * FSL 
 +  * AFNI 
 +  * pyMVPA 
 +  * nibabel 
 +  * mricron 
 +  * psychtoolbox 
 +  * odds and ends, converters, viewers and so on.
  
-- FileZilla (https://filezilla-project.org/) + 
-- GCC version to 4.8 if possible (https://gcc.gnu.org/gcc-4.8/) +=== Utilities === 
-- R + 
-- Rminc +  * apticron 
-- Slack +  * Anaconda, miniconda and conda 
-- zlib (http://www.zlib.net/)+  * 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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 * [[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.1497372530.txt.gz
  • Last modified: 2024/03/26 13:52
  • (external edit)