Class: DefaultRecon::PfileRawSequence

Inherits:
RawSequence show all
Defined in:
lib/default_methods/recon/raw_sequence.rb

Overview

Reconstucts a PFile from Raw to Nifti File

Instance Method Summary collapse

Constructor Details

#initialize(scan_spec, rawdir) ⇒ PfileRawSequence

Create a local unzipped copy of the Pfile and prepare Scanner Reference Data for reconstruction

Raises:

  • (IOError) 


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# File 'lib/default_methods/recon/raw_sequence.rb', line 70

def initialize(scan_spec, rawdir)
  super(scan_spec, rawdir)
  
  base_pfile_path = File.join(@rawdir, @scan_spec['pfile'])
  pfile_path = File.exist?(base_pfile_path) ? base_pfile_path : base_pfile_path + '.bz2'
  
  raise IOError, "#{pfile_path} does not exist." unless File.exist?(pfile_path)
  
  flash "Pfile Reconstruction: #{pfile_path}"
  @pfile_data = Pathname.new(pfile_path).local_copy
  
  @refdat_file = @scan_spec['refdat_stem'] ||= search_for_refdat_file
  setup_refdat(@refdat_file)
end

Instance Method Details

#reconstruct_sequence(outfile) ⇒ Object Also known as: prepare

Reconstructs a single pfile using epirecon Outfile may include a ‘.nii’ extension - a nifti file will be constructed directly in this case.

Raises:

  • (ScriptError) 


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# File 'lib/default_methods/recon/raw_sequence.rb', line 88

def reconstruct_sequence(outfile)
  volumes_to_skip = @scan_spec['volumes_to_skip'] ||= 3
  epirecon_cmd_format = "epirecon_ex -f %s -NAME %s -skip %d -scltype=0"
  epirecon_cmd_options = [@pfile_data, outfile, volumes_to_skip]
  epirecon_cmd = epirecon_cmd_format % epirecon_cmd_options
			raise ScriptError, "Problem running #{epirecon_cmd}" unless run(epirecon_cmd)
end