Computer Setup
Page Contents
Computer Setup#
Modify User Template#
Go under:
/System/Library/User\ Template/English.lproj
Shell Profile #
You can edit your shell profile (usually called .bash_profile
, but some newer versions of Mac use .zsh_profile
) to create custom commands and make the colours in your terminal look nice.
To edit, navigate to $HOME/.bash_profile
# Nice .bash_profile
# COLOR
export CLICOLOR=1
export LSCOLORS=GxFxCxDxBxegedabagaced
# PROMPT
PS1='\[\e[1;31m\]\h:\[\e[m\]\[\e[0;36m\]\w\[\e[m\] \[\e[0;38m\]\$ \[\e[m\]\[\e[0;38m\]'
# ALIAS
alias ll="ls -la"
alias edit="open -a textedit"
alias matlab="/Applications/MATLAB_R2020a.app/bin/matlab &"
alias test_sct="/Users/julien/code/spinalcordtoolbox/testing/test_all.py"
alias abbey="ssh p101317@abbey.neuro.polymtl.ca"
alias django="ssh jcohen@django.neuro.polymtl.ca"
alias davis="ssh jcohen@davis.neuro.polymtl.ca"
alias rosenberg="ssh p101317@rosenberg.neuro.polymtl.ca"
alias bireli="ssh p101317@bireli.neuro.polymtl.ca"
alias joplin="ssh p101317@joplin.neuro.polymtl.ca"
alias guillimin="ssh jcohen@guillimin.hpc.mcgill.ca"
alias cedar="ssh jcohen@cedar.computecanada.ca"
alias graham="ssh jcohen@graham.computecanada.ca"
alias niagara="ssh jcohen@niagara.computecanada.ca"
alias gs="git status -s"
alias gc="git commit -S -a"
alias gp="git push"
alias gl="git log --pretty=oneline"
alias glg="git log --pretty=oneline --decorate --all --graph"
alias gd="git diff"
alias gb="git branch"
# FSL Setup
FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh
# FSLeyes
PATH=${PATH}:/Applications/FSLeyes.app/Contents/MacOS
# DCM2NII
PATH=${PATH}:/Applications/mricron
# ANTS
PATH=${PATH}:/usr/local/ants/bin
# cmake
export PATH=${PATH}:/Applications/CMake.app/Contents/bin
# MINICONDA
export PATH="$HOME/miniconda3/bin:$PATH" # commented out by conda initialize
source ~/miniconda3/etc/profile.d/conda.sh
To edit, navigate to $HOME/.zsh_profile
# COLOR
export CLICOLOR=1
export LSCOLORS=GxFxCxDxBxegedabagaced
# PROMPT
PS1='%B%F{red}%m:%F{cyan}%~ %F{white}$ '
# ALIAS
alias ll="ls -la"
alias edit="open -a textedit"
alias matlab="/Applications/MATLAB_R2020a.app/bin/matlab &"
alias test_sct="/Users/julien/code/spinalcordtoolbox/testing/test_all.py"
alias abbey="ssh p101317@abbey.neuro.polymtl.ca"
alias django="ssh jcohen@django.neuro.polymtl.ca"
alias davis="ssh jcohen@davis.neuro.polymtl.ca"
alias rosenberg="ssh p101317@rosenberg.neuro.polymtl.ca"
alias bireli="ssh p101317@bireli.neuro.polymtl.ca"
alias joplin="ssh p101317@joplin.neuro.polymtl.ca"
alias guillimin="ssh jcohen@guillimin.hpc.mcgill.ca"
alias cedar="ssh jcohen@cedar.computecanada.ca"
alias graham="ssh jcohen@graham.computecanada.ca"
alias niagara="ssh jcohen@niagara.computecanada.ca"
alias gs="git status -s"
alias gc="git commit -S -a"
alias gp="git push"
alias gl="git log --pretty=oneline"
alias glg="git log --pretty=oneline --decorate --all --graph"
alias gd="git diff"
alias gb="git branch"
# FSL Setup
FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh
# FSLeyes
PATH=${PATH}:/Applications/FSLeyes.app/Contents/MacOS
# DCM2NII
PATH=${PATH}:/Applications/mricron
# ANTS
PATH=${PATH}:/usr/local/ants/bin
# cmake
export PATH=${PATH}:/Applications/CMake.app/Contents/bin
# MINICONDA
export PATH="$HOME/miniconda3/bin:$PATH" # commented out by conda initialize
source ~/miniconda3/etc/profile.d/conda.sh
niftiviewer.app #
UPDATE: NO NEED TO DO THE THING BELOW ANYMORE WITH NIFTI. Instead, right click > βget infoβ > Open with > change allβ¦ > select fsleyes
In automator, create new application - run apple script. Add the following script:
on run {input, parameters}
set f to POSIX path of (input as text)
do shell script "source ~/.bash_profile"
do shell script "open -n -a fslview.app --args " & f
end run
Select .nii file β open with β> select niftiviewer.app
Add LINUX machine to GRAMES #
See info under Gdrive/Neuropoly/network/SOP_add_linux_station_grames.docx
Configure virtualenvwrapper under LINUX #
Add script under /etc/profile.d/virtual_env_config.sh :
export WORKON_HOME=$HOME/.virtualenvs
export PROJECT_HOME=$HOME/
source /usr/local/bin/virtualenvwrapper.sh #centos
source /usr/share/virtualenvwrapper/virtualenvwrapper.sh #ubuntu
Update debian 7 to 8 #
https://www.prado.lt/how-to-upgrade-debian-7-wheezy-to-10-buster-safely