software_listing
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software_listing [2017/03/14 17:56] csteel |
software_listing [2018/01/30 14:30] 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 | ||
| + | * openmp | ||
| + | * RMINC [[https://github.com/Mouse-Imaging-Centre/RMINC]] | ||
| + | * SPM | ||
| + | * 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 === | ||
| Line 7: | Line 118: | ||
| * [[http://bic-mni.github.io/]] | * [[http://bic-mni.github.io/]] | ||
| * [[http://bic-mni.github.io/#version-10081008-currently-stable]] | * [[http://bic-mni.github.io/#version-10081008-currently-stable]] | ||
| + | |||
| + | == MINC Metaproject | ||
| + | |||
| + | Metaproject uniting all the available minc tools | ||
| + | |||
| + | * [[https://github.com/BIC-MNI/minc-toolkit]] | ||
| + | |||
| == MINC References | == MINC References | ||
| Line 12: | Line 130: | ||
| * [[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 === | ||
| Line 27: | Line 149: | ||
| * [[https://github.com/Mouse-Imaging-Centre/pydpiper]] < Preferred? | * [[https://github.com/Mouse-Imaging-Centre/pydpiper]] < Preferred? | ||
| + | * [[http://www.mouseimaging.ca/]] | ||
| * [[https://github.com/bcdarwin/pydpiper]] | * [[https://github.com/bcdarwin/pydpiper]] | ||
| * [[https://github.com/psteadman/pydpiper]] | * [[https://github.com/psteadman/pydpiper]] | ||
| Line 34: | Line 157: | ||
| === 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 === | ||
| - | (latest version, which is maintained by Mouse Imaging Centre - Jason Lerch and others) | + | Statistics for MINC volumes: A library to integrate voxel-based statistics for MINC volumes into the R environment. Supports getting and writing of MINC volumes, running voxel-wise linear models, correlations, etc.; correcting for multiple comparisons using the False Discovery Rate, and more. With contributions from Jason Lerch, Jim Nikelski and others |
| * [[https://github.com/Mouse-Imaging-Centre/RMINC|RMINC]] | * [[https://github.com/Mouse-Imaging-Centre/RMINC|RMINC]] | ||
| + | |||
| === Matlab === | === Matlab === | ||
| Line 77: | Line 218: | ||
| * [[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.txt · Last modified: 2018/01/30 14:34 by xteng
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