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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
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
Zotero + Word extension	manuscript authoring
Chrome + Zotero extension	manuscript authoring
python	statistical analysis
Git tools	software programming
Horos (dicom viewer)	MR (raw) 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)"