Version: 0.2.0

Installation

git clone https://github.com/Microdeep-ZL/bruker2bids.git
conda create -n bruker2bids -c conda-forge dcm2niix nodejs

dependecies

• node.js and dcm2niix
  • can be installed via conda
• pigz, tree, zip
  • If you don't have sudo privilege to install them, try these two workarounds
    • If you are using CentOS or Red Hat, user-yum.sh is recommended
    • Otherwise

     # add the following lines to your ~/.bashrc
     function tree(){
         path=.
         if [ -n $1 ]
             then path="$@"
         fi
         find $path -print | sed -e "s;[^/]*/;|____;g;s;____|; |;g"
     }
    
     alias pigz=gzip

• singularity and FSL singularity container
  • optional, can be ignored if you are not using the reorientation feature

Quick start

# add this function to your ~/.bashrc
# <bruker2bids> is the path to this git repository
# <bruker data directory> is the diectory inside which you can find
#   folders like "20230309_115904_mrmdPractice4052DREADD_1_1" etc
function bruker2bids(){
	cd <bruker2bids>
	conda activate bruker2bids
	node main.js <bruker data directory>
}

Features

• straightforward GUI based on web
• Automated BIDS conversion as you scan
• help you enable port forwarding when using bruker2bids through SSH
• wildcards and list support in criteria
• immediate preview of BIDS result
• immediate preview of scan parameters
• zip or tar.gz the result with one click
• automatic run label for scans with identical labels according to their chronological order
• No interference between mutiple users
• reorient images with one click
• save, load and delete your own config files

Demo

https://mrmdlab.github.io/products/#bruker2bids

License

Apache-2.0