Differences

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--- software_listing [2017/08/14 18:59] – csteel
+++ software_listing [2024/03/26 13:52] (current) – external edit 127.0.0.1
@@ Line 4: / Line 4: @@
   * Anaconda v4.2 for Python 2.7 (https://www.continuum.io/downloads)
-  * AFNI (
+  * AFNI
   * ANTs (http://stnava.github.io/ANTs/)
+  * BEaST
   * BigBrain on line (https://bigbrain.loris.ca/main.php)
   * BrainSuite16a1 (http://brainsuite.org/)
+  * BrainView
+  * Caret
   * CIVET
-  * Deformation fields
+  * 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)
@@ Line 15: / Line 19: @@
   * 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
-  * Mricron tools (http://people.cas.sc.edu/rorden/mricron/install.html)
+    * 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/)
@@ Line 65: / Line 130: @@
 * [[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 ===
@@ Line 88: / Line 157: @@
 === Development, Programming and Scripting ===
+  * adacity
+  * build-essential
   * C
+  * cmake
+  * filezilla
   * GNC Make
+  * gparted
+  * latex
+  * pbzip, pigz, rar, p7zip-full
+  * pdftk, qpdf
   * Perl
   * Python
+  * imagemagick
   * R
+  * renameutils
+  * scribus
+  * sox
+  * sshfs
+  * tree
+  * vim
+  * Virtualbox
+  * watch
 === RMINC ===
@@ Line 132: / Line 218: @@
 * [[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 ===