Module: UnknownImageDataset

Defined in:
lib/metamri/nifti_builder.rb

Overview

Builds Nifti files from Dicoms.

Instance Method Summary collapse

Instance Method Details

#dataset_to_nifti(nifti_output_directory, nifti_filename, input_options = {}) ⇒ Object

Raises:

  • (IOError) 


8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
 
# File 'lib/metamri/nifti_builder.rb', line 8

def dataset_to_nifti(nifti_output_directory, nifti_filename, input_options = {} )
  if input_options.has_key?(:dicom_files)
    input_files = input_options[:dicom_files].each {|file| file.to_s }.join(' ')
  elsif input_options.has_key?(:input_directory)
    input_files = "#{input_options[:input_directory]}/'#{glob}'"
  else input_files = "#{Dir.tmpdir}/'#{glob}'"
  end
  
  if @raw_image_files.first.rep_time && @raw_image_files.first.bold_reps && @raw_image_files.first.num_slices && !input_options[:no_timing_options]
    slice_order = "altplus"
    functional_args = "-time:zt #{@raw_image_files.first.num_slices} #{@raw_image_files.first.bold_reps} #{@raw_image_files.first.rep_time} #{slice_order}"
  end
  
  
  nifti_output_file = File.join(nifti_output_directory, nifti_filename)
  
  FileUtils.makedirs(nifti_output_directory) unless File.directory?(nifti_output_directory)
  raise(IOError, "Cannot write to #{nifti_output_directory}") unless File.writable?(nifti_output_directory)
      
  nifti_conversion_command = "to3d -session #{nifti_output_directory} -prefix #{[nifti_filename, functional_args, input_files].compact.join(' ')}"

  return nifti_conversion_command, nifti_output_file
end