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Wrapper to compute symmetric transform and BSI, running in a batch.

Usage: /scratch0/NOT_BACKED_UP/clarkson/auto/src/niftk-nightly-release/NifTK-build/bin/compute_symmetric_transform_batch.sh input_csv_file output_dir [options]

Mandatory Arguments:

  input_csv_file    : An input csv file containing the following format:
                      baseline_image,baseline_region,baseline_dof,repeat_image,repeat_region,repeat_dof
                    
                      Full paths should be specified. Images are assumed to be uncompressed.
                    
  output_dir        : Output directory
                    
Optional Arguments:                     
  -tp3                  : for 3 time points (old format). 
  -tpn                  : for n time points. 
  -interpolation i      : NN: 1, linear: 2, cubic: 3, sinc: 4. 
  -double_window yes/no : double window or not. 
  -ss_atlas dummy       : atlas used to generate img from midas region. 
  -just_dbc yes/no      : just do dbc without transformation if yes. 
  -kernel i             : specify the size of kernel for DRC, default: 5
  -dbc_mode i           : mode to run dbc in: 1= from all images, 2= from consective TPs
  -pairwise_dbc i       : pairwise dbc if 1, groupwise dbc if 0 (default).