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convert Paravision v6.0.1 data into BIDS with straightforward GUI

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mrmdlab/bruker2bids

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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

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convert Paravision v6.0.1 data into BIDS with straightforward GUI

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