Module: JohnsonTbiLongitudinalSnodStats

Defined in:
lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb

Overview

require ‘logfile’

Constant Summary collapse

DEFAULT_CONDITIONS = 
[:new, :old]

Instance Method Summary collapse

Instance Method Details



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# File 'lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb', line 29

def create_or_link_onsets_files
  if @onsetsfiles.nil?
  if @responses.nil?
    raise ScriptError, "Condition vectors cannot be created because neither log response files nor onsets mat files have been specified."
   else
     @onsetsfiles = create_onsets_files(@responses, conditions)
    end
  else
   link_onsets_files
end
end

#run_first_level_stats ⇒ Object Also known as: perform

runs the complete set of tasks using data in a subject’s “proc” directory and a preconfigured template spm job.



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# File 'lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb', line 7

def run_first_level_stats
	flash "Highway to the dangerzone..."
	setup_directory(@statsdir, "STATS")
	
	Dir.chdir(@statsdir) do
		link_files_from_proc_directory(File.join(@procdir, "sw*.nii"), File.join(@procdir, "rp*.txt"))
		setup_onsets
		run_stats_spm_job
	end
end

#run_stats_spm_job ⇒ Object

Finally runs the stats job

Raises:

  • (ScriptError) 


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# File 'lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb', line 42

def run_stats_spm_job
  images = @scan_labels ? @scan_labels.collect! { |label| Dir.glob("sw*#{label}*.nii").to_s } : Dir.glob(File.join(@origdir, "sw*#{@subid}*.nii"))
  raise ScriptError, "Can't find any smoothed, warped images in #{@statsdir}" if images.empty?
  unless @onsetsfiles.length == @regressorsfiles.length && @regressorsfiles.length == @bold_reps.length
    raise ScriptError, "Mismatch between #{@bold_reps.length} reps, #{@onsetsfiles.length} onsets and #{@regressorsfiles.length} regressors files."
  end
  
  queue = MatlabQueue.new
 queue.paths << [
   '/Applications/spm/spm8/spm8_current', 
   '/apps/spm/spm8_current',
    File.join(@libdir, 'custom_methods'), 
    File.join(@libdir, 'matlab_helpers')    ]

 queue << "JohnsonTbiLongitudinalSnodStats('#{@statsdir}/', \
  { #{images.collect {|im| "'#{File.basename(im)}'"}.join(' ')} },  \
  { #{@bold_reps.join(' ') } }, \
  { #{@onsetsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
  { #{@regressorsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
  'JohnsonTbiLongitudinalSnodStats_job.m')"
  
  # puts queue.to_s
  queue.run!
end

#setup_conditions ⇒ Object 



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# File 'lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb', line 25

def setup_conditions
  @conditions = @conditions ? @conditions.collect {|c| c.to_sym if c.respond_to? :to_sym } : DEFAULT_CONDITIONS 
end

#setup_onsets ⇒ Object 



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# File 'lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb', line 20

def setup_onsets
 setup_conditions
  create_or_link_onsets_files
end