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LNCD Software

Homegrown

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

Here's a list of external software used for research. This is ideal reference for OAC Administered Systems. Also see awesome-neuroimaging list

package	why
Adobe Illustrator, Acrobat	figure editing
MS Office	manuscript authoring
Matlab (Fieldtrip, SPM, PsychToolbox)	MR and EEG analysis, behavioral task edit/inspect

package	why
R + Rstudio	statistical analysis
AFNI	MR analysis and visualization
DSIstudio	MR (DSI) analysis and visualization
Connectome Workbench	MR (surface) analysis and visualization
Zotero + Word extension	manuscript authoring
Chrome + Zotero extension	manuscript authoring
python	statistical analysis
Git tools	software programming
Horos	MR (raw/DICOM) visualization
Slack desktop	Pitt collaboration and communication
Zoom	Collaboration and communication

on MacOS, lower level dependencies for above include

package	why
xcode ¹⁾	afni depends(homebrew) and R libaries (compiling)
homebrew ²⁾: python, gfortran, libxml, netpbm, openblas, lapack	AFNI, R library compiling
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)"