brainwhere

KO | EN

gitlite — search

#python #golang #go #machine-learning #linux #docker #macos #java #windows #awesome #cli #kubernetes #vue #ios

(★ 10)

A repository for my neuroimaging scripts and resources. Heavy on the FSL and AFNI.

brainwhere Latest Version Download

Download Latest Version (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

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.](http://j.mp/setupScripting)
2. Install FSL, AFNI, and BXH/XCEDE. You may want to refer to [my instructions.](http://j.mp/setupNeuroimaging)
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.

brainwhere

brainwhere Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

brainwhere

brainwhere Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

Download README