brainwhere

brainwhere: a repository for my neuroimaging scripts and resources

• It's mostly bash scripts.
• Heavy lifting by FSL, AFNI, FREESURFER, FBIRN.
• Two goals: make the science, support my training of new imagers.

STATUS:

Jan/Feb 2015: Still just for my use, still porting to github.

INSTALLATION:

It may destroy your data and computer and everything attached to it, but with attribution you are welcome to use this for non-clinical purposes. Please consider all code proof-of-concept-dangerous, and test thoroughly in a safe environment.

1. Install this basic set of system utilities.
2. Install FSL, AFNI, and BXH/XCEDE. You may want to refer to my instructions.
3. Install the brainwhere repository by cloning it with git. Here's how:

(It is safer to paste these into your terminal line-by-line rather than as a block:)

# =================================================================================================
# STEP 1/5: Set installation directory (for my local OS X and linux installs: bwParentDir=/opt )
#
bwParentDir=[where you would like the directory called brainwhere to reside]

# =================================================================================================
# STEP 2/5: Test whether you have permissions to write to ${bwParentDir} :
#
cd ${bwParentDir}
sudo touch doIhavePermissionsToWriteHere.txt 
ls -l doIhavePermissionsToWriteHere.txt
sudo rm doIhavePermissionsToWriteHere.txt

# =================================================================================================
# STEP 3/5: If that worked, just install from github:
#
cd ${bwParentDir}
sudo git clone https://github.com/stowler/brainwhere.git
export bwDir=${bwParentDir}/brainwhere
ls ${bwDir}

# =================================================================================================
# STEP 4/5: Add brainwhere's new location to the path in your system-wide bash config file:
#
#    WARNING: note the \${escapedVariables} below, which
#    are escaped for heredoc (http://goo.gl/j3HMJ). 
#    Un-escape them if manually typing into a text editor.
#    Otherwise, just paste these lines to your bash prompt
#    (up to and including "EOF" line):
#
mySystemBashConfig=/etc/bash.bashrc    #debian is /etc/bash.bashrc , ubuntu and lion are /etc/bashrc
editDate=`/bin/date +%Y%m%d`
editTime=$(date +%k%M)
sudo tee -a ${mySystemBashConfig} >/dev/null <<EOF
#------------------------------------------
# on ${editDate} at ${editTime}, $USER  
# added some brainwhere environmental variables:
export bwDir=$bwDir
export PATH=\${bwDir}:\${PATH}
#------------------------------------------
EOF

# =================================================================================================
# STEP 5/5: Confirm that the system-wide access works:
#
cat ${mySystemBashConfig}
# open a new terminal window and confirm $bwDir:
ls $bwDir
echo $PATH

NB: As in these installation instructions, you may notice that the source code is structured and commented for users who have a wide range of comfort with scripting. I use this repository to make science and train new imagers, which doesn't produce the prettiest or most efficient code.