====== LNCD Software ======
===== Homegrown =====
R, generic, and shell tools made specifically for our research

  * [[https://github.com/LabNeuroCogDevel/LNCDR|LNCDR]] (''date_match'')
  * [[https://github.com/LabNeuroCogDevel/lncdtools|lncdtools]] on wiki [[tools:lncdtools]] (''mkls'' for [[tools:make]], ''waitforjobs'', ''dryrun'' and ''warn'' for [[tools:shell]])

===== External =====
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 ^
|Adobe Illustrator, Acrobat  | figure editing |
|MS Office | manuscript authoring  |
|Matlab (Fieldtrip, SPM, PsychToolbox) | MR and EEG analysis, behavioral task edit/inspect  |
|Slack desktop               | Pitt 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 ====
on MacOS, lower level dependencies for above include
^package ^ why ^
|xcode ((<code=shell>xcode-select --install</code>)) | afni depends(homebrew) and R libaries (compiling) |
|[[https://brew.sh/|homebrew]] ((<code>/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
 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 |