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 Read further if:

  • you develop or run image processing locally in bash;
  • you want to use XNAT as data source and/or remote archive;
  • you want to automate processing of multiple XNAT sessions and want to report your results in spreadsheets.

Use case: compute BET whole brain volume for all MPRAGE scans in an MRI project in XNAT and save statistics in a spreadsheet.

  1. write a bash script (assuming FSL is on the path).

    brain_volume.sh
    #!/bin/bash
    in=$1 #input DICOM scan
    dcm2nii $in
    cp $in/[0-9]*.nii head.nii
    if [ ! -f "head.nii" ]; then exit -1; fi
    bet head brain -m
    vol=(`fslstats brain_mask -V`); vol=${vol[1]}
    #report the volume in mm3 to console.
    echo $vol
    
    

 

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