LNCD Software

Homegrown

R, generic, and shell tools made specifically for our research

LNCDR (date_match)
lncdtools on wiki LNCD Tools (mkls for make, waitforjobs, dryrun and warn for Shell)

External

Here's a list of external software used for research. This is ideal reference for OAC Administered Systems. Also see awesome-neuroimaging list and 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
R + Rstudio	statistical analysis
AFNI	MR analysis and visualization
FSL	MR analysis and visualization (`fsleyes`)
DSIstudio	MR (DSI) analysis and visualization
Connectome Workbench	MR (surface) analysis and visualization
freesurfer	MR (anatomical) analysis and visualization
Zotero + Word extension	manuscript authoring
Chrome + Zotero extension	manuscript authoring
Horos	MR (raw/DICOM) visualization
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 ¹⁾	afni depends(homebrew) and R libaries (compiling)
homebrew ²⁾	AFNI, R library compiling, singluarity image
Xquartz	AFNI and ssh X11-forwarding

¹⁾

xcode-select --install

²⁾

/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