Module: DefaultRecon

Included in:
Reconstruction
Defined in:
lib/default_methods/default_recon.rb,
lib/default_methods/recon/raw_sequence.rb,
lib/default_methods/recon/physionoise_helper.rb

Overview

require ‘default_methods/recon/physionoise_helper’

Defined Under Namespace

Classes: DicomRawSequence, PfileRawSequence, RawSequence

Instance Method Summary collapse

Instance Method Details

#build_physionoise_run_spec(rpipe_scan_spec) ⇒ Object

Build a Run Spec from a Scan Spec This should be moved to the generators and shouldn’t be used here.



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# File 'lib/default_methods/recon/physionoise_helper.rb', line 19

def build_physionoise_run_spec(rpipe_scan_spec)
  run = rpipe_scan_spec['physio_files'].dup
  flash "Physionoise Regressors: #{run[:phys_directory]}"
  run[:bold_reps] = rpipe_scan_spec['bold_reps']
  run[:rep_time] = rpipe_scan_spec['rep_time']
  unless Pathname.new(run[:phys_directory]).absolute?
    run[:phys_directory] = File.join(@rawdir, run[:phys_directory])
  end
  run[:run_directory] = @rawdir
  runs = [run]
end

#build_retroicor_cmd(physio_files, file) ⇒ Object

:respiration_trigger: RESPTrig_epiRT_0303201014_46_27_463

:phys_directory: cardiac/
:cardiac_signal: PPGData_epiRT_0303201014_46_27_463
:cardiac_trigger: PPGTrig_epiRT_0303201014_46_27_463



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# File 'lib/default_methods/recon/physionoise_helper.rb', line 52

def build_retroicor_cmd(physio_files, file)
  [:cardiac_signal, :respiration_signal].collect {|req| raise ScriptError, "Missing physio config: #{req}" unless physio_files.include?(req)}
  
  prefix = 'p'
  unless Pathname.new(physio_files[:cardiac_signal]).absolute?
    cardiac_signal = File.join(@rawdir, physio_files[:phys_directory], physio_files[:cardiac_signal])
  end
  
  unless Pathname.new(physio_files[:respiration_signal]).absolute?
    respiration_signal = File.join(@rawdir, physio_files[:phys_directory], physio_files[:respiration_signal])
  end
  
  outfile = prefix + file

  icor_format = "3dretroicor -prefix %s -card %s -resp %s %s"
  icor_options = [outfile, cardiac_signal, respiration_signal, file]
  icor_cmd = icor_format % icor_options
  return icor_cmd, outfile
end

#create_physiosnoise_regressors(scan_spec) ⇒ Object

Create Physionoise Regressors for Inclusion in GLM



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# File 'lib/default_methods/recon/physionoise_helper.rb', line 6

def create_physiosnoise_regressors(scan_spec)
  runs = build_physionoise_run_spec(scan_spec)
  Physionoise.run_physionoise_on(runs, ["--saveFiles"])
end

#generate_physiospec ⇒ Object

Generate a Physionoise Spec



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# File 'lib/default_methods/recon/physionoise_helper.rb', line 12

def generate_physiospec
 physiospec = Physiospec.new(@rawdir, File.join(@rawdir, '..', 'cardiac'))
 physiospec.epis_and_associated_phys_files
end

#recon_visit ⇒ Object Also known as: perform

Reconstructs, strips, and slice timing corrects all scans specified in the recon_spec. This function assumes a destination directory is set up in the filesystem and begins writing to it with no further checking. It will overwrite data if it already exists, be careful.



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# File 'lib/default_methods/default_recon.rb', line 11

def recon_visit
	
	setup_directory(@origdir, "RECON")
	
	Dir.chdir(@origdir) do		  
		@scans.each_with_index do |scan_spec, i|
			outfile = "%s_%s.nii" % [@subid, scan_spec['label']]
			
			reconstruct_scan(scan_spec, outfile)
			
			if scan_spec['type'] == "func"
         # if scan_spec['physio_files']
         #   create_physiosnoise_regressors(scan_spec)
         #   outfile = run_retroicor(scan_spec['physio_files'], outfile)
         # end
			  
				slice_time_correct(outfile)
			else
				File.copy('tmp.nii', outfile)
			end
			
			File.delete('tmp.nii') if File.exist? 'tmp.nii'
		end
	end
end

#reconstruct_scan(scan_spec, outfile) ⇒ Object

Reconstructs a scan from dicoms or pfile to nifti, anatomical or functional. Uses a scan_spec hash to drive. Writes the result in current working directory. Raises an error if to3d system call fails. Conventions: I****.dcm filenaming, I0002.dcm is second file in series,



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# File 'lib/default_methods/default_recon.rb', line 43

def reconstruct_scan(scan_spec, outfile)	
	if scan_spec['dir']
	  sequence = DicomRawSequence.new(scan_spec, @rawdir)
	  sequence.prepare('tmp.nii')
		strip_leading_volumes('tmp.nii', outfile, @volume_skip, scan_spec['bold_reps'])
  elsif scan_spec['pfile']
    sequence = PfileRawSequence.new(scan_spec, @rawdir)
    sequence.prepare(outfile)
   else 
     raise ConfigError, "Scan must list either a pfile or a dicom directory."
   end
end

#run_retroicor(physio_files, file) ⇒ Object

Runs 3dRetroicor for a scan. Returns the output filename if successful or raises an error if there was an error.



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# File 'lib/default_methods/recon/physionoise_helper.rb', line 33

def run_retroicor(physio_files, file)
 icor_cmd, outfile = build_retroicor_cmd(physio_files, file)
 flash "3dRetroicor: #{file} \n #{icor_cmd}"
 if run(icor_cmd)
   return outfile
  else
    raise ScriptError, "Problem running #{icor_cmd}"
  end
end

#slice_time_correct(infile) ⇒ Object

Uses to3d to slice time correct a 4D functional nifti file. Writes result in the current working directory.



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# File 'lib/default_methods/default_recon.rb', line 69

def slice_time_correct(infile)
	$Log.info "Slice Timing Correction: #{infile}"
	cmd = "3dTshift -tzero 0 -tpattern alt+z -prefix a#{infile} #{infile}"
	unless run(cmd)
	  raise ScriptError, "Failed to slice time correct: #{cmd}"
  end
end

#strip_leading_volumes(infile, outfile, volume_skip, bold_reps) ⇒ Object

Removes the specified number of volumes from the beginning of a 4D functional nifti file. In most cases this will be 3 volumes. Writes result in current working directory.



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# File 'lib/default_methods/default_recon.rb', line 58

def strip_leading_volumes(infile, outfile, volume_skip, bold_reps)
	$Log.info "Stripping #{volume_skip.to_s} leading volumes: #{infile}"
	cmd_fmt = "fslroi %s %s %s %s"
	cmd_options = [infile, outfile, volume_skip.to_s, bold_reps.to_s]
	cmd = cmd_fmt % cmd_options
	unless run(cmd)
	  raise ScriptError, "Failed to strip volumes: #{cmd}"
  end
end