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tools:software [2024/05/28 11:03] – add external willtools:software [2026/09/29 12:31] (current) – [LNCD Software] will
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 ====== LNCD Software ====== ====== LNCD Software ======
 +Also see [[admin:software:researcher]] for a new computer software install check list
 ===== Homegrown ===== ===== Homegrown =====
 R, generic, and shell tools made specifically for our research R, generic, and shell tools made specifically for our research
  
-  * [[https://github.com/LabNeuroCogDevel/LNCDR|LNCDR]] (date_match) +  * [[https://github.com/LabNeuroCogDevel/LNCDR|LNCDR]] (''date_match'') 
-  * [[https://github.com/LabNeuroCogDevel/lncdtools|lncdtools]] on wiki [[tools:lncdtools]] (mkls for [[tools:make]], dryrun and warn for [[tools:shell]]) +  * [[https://github.com/LabNeuroCogDevel/lncdtools|lncdtools]] on wiki [[tools:lncdtools]] (''mkls'' for [[tools:make]], ''waitforjobs'', ''dryrun'' and ''warn'' for [[tools:shell]])
-  * [[https://github.com/LabNeuroCogDevel/lncdshell|lncdshell]] (waitforjobs)+
  
 ===== External ===== ===== External =====
-Here's a list of external software used for research. This is ideal reference for OAC Administered Systems.+Here's a list of external software used for research. This is ideal reference for OAC Administered Systems. Also see [[https://github.com/NPACore/awesome-neuroimaging|awesome-neuroimaging list]] and [[https://github.com/NPACore/NPACore.github.io/blob/main/docs/projects/software/macos-admin.bash|Mac OS OAC install script]]
  
 +
 +==== Commercial software ====
 ^package ^ why ^ ^package ^ why ^
 |Adobe Illustrator, Acrobat  | figure editing | |Adobe Illustrator, Acrobat  | figure editing |
-|Matlab (Fieldtrip, SPM, PsychToolbox) | MR and EEG analysis, behavioral task edit/inspect  | 
-|R + Rstudio                    | statistical analysis | 
-|AFNI                        | MR analysis and visualization | 
-|DSIstudio                   | MR (DSI) analysis and visualization | 
-|Connectome Workbench        | MR (surface) analysis and visualization | 
 |MS Office | manuscript authoring  | |MS Office | manuscript authoring  |
-|Zotero + Word extension     | manuscript authoring | +|Matlab (Fieldtrip, SPM, PsychToolbox) | MR and EEG analysis, behavioral task edit/inspect  |
-|Chrome + Zotero extension   | manuscript authoring| +
-|python                      | statistical analysis| +
-|Git tools                   | software programming| +
-|Horos (dicom viewer)        | MR (raw) visualization|+
 |Slack desktop               | Pitt collaboration and communication| |Slack desktop               | Pitt collaboration and communication|
 |Zoom                        | Collaboration and communication| |Zoom                        | Collaboration and communication|
 +
 +
 +==== Open Source ====
 +^package ^ why ^
 +|[[https://cran.r-project.org/bin/macosx/|R]] + [[https://posit.co/download/rstudio-desktop/|Rstudio]]  | statistical analysis |
 +|[[https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_admins/steps_mac_Admin.html|AFNI]]| MR analysis and visualization |
 +|[[https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation|FSL]] | MR analysis and visualization (''fsleyes'')|
 +|[[https://dsi-studio.labsolver.org/download.html|DSIstudio]]                   | MR (DSI) analysis and visualization |
 +|[[https://www.humanconnectome.org/software/get-connectome-workbench#download|Connectome Workbench]]        | MR (surface) analysis and visualization |
 +|[[https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads|freesurfer]] |MR (anatomical) analysis and visualization|
 +|[[https://www.zotero.org/download/|Zotero]] + Word extension     | manuscript authoring |
 +|Chrome + Zotero extension   | manuscript authoring|
 +|[[https://horosproject.org/download-donation/|Horos]] | MR (raw/DICOM) visualization|
 +|[[https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-on-windows-or-mac|singularity]]| collaboration and software reuse|
 +|python                      | statistical analysis (via homebrew)|
 +|Git tools                   | software programming (via homebrew)|
  
  
 ==== Dependencies ==== ==== Dependencies ====
 +on MacOS, lower level dependencies for above include
 ^package ^ why ^ ^package ^ why ^
-|xcode | afni depends(homebrew) and R libaries (compiling) | +|xcode ((<code=shell>xcode-select --install</code>)) | afni depends(homebrew) and R libaries (compiling) | 
-|homebrew: python, gfortran, libxml, netpbm, openblas, lapack | AFNI, R library compiling | +|[[https://brew.sh/|homebrew]] ((<code>/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)" 
-|Xquartz | AFNI and ssh X11-forwarding |+ brew install python gfortran libxml++ netpbm openblas lapack openconnect vagrant{,-manager} # virtualbox</code>)) | AFNI, R library compiling, singluarity image | 
 +|[[https://www.xquartz.org/|Xquartz]] | AFNI and ssh X11-forwarding |