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#!/usr/bin/env ruby =begin rdoc Builds Nifti files from Dicoms. =end module UnknownImageDataset # Always set AFNI GE DICOM Fix to "No" before conversion with to3d. ENV['AFNI_SLICE_SPACING_IS_GAP'] = "NO" 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) File.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 end module DTIDataset def dataset_to_nifti(nifti_output_directory, nifti_filename, input_options = {} ) end end
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11 entries across 11 versions & 1 rubygems