lib/metamri/nifti_builder.rb in metamri-0.1.17 vs lib/metamri/nifti_builder.rb in metamri-0.1.18

@@ -16,21 +16,21 @@
     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
+    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}"
+    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
 
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