fsl-ruby 0.0.1

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in fsl-ruby.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2012 Simon Rascovsky
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Fsl::Ruby
+
+A Ruby wrapper for the FSL neuroimaging suite
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'fsl-ruby'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install fsl-ruby
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/fsl-ruby.gemspec

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+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'fsl-ruby/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "fsl-ruby"
+  gem.version       = FSL::VERSION
+  gem.authors       = ["Simon Rascovsky"]
+  gem.email         = ["simonmd@gmail.com"]
+  gem.description   = %q{Ruby Wrapper for the FSL Neuroimaging suite}
+  gem.summary       = %q{Ruby Wrapper for the FSL Neuroimaging suite}
+  gem.homepage      = ""
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+end

data/lib/fsl-ruby.rb

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+require "fsl-ruby/version"
+require "fsl-ruby/bet"
+require "fsl-ruby/first"
+require "fsl-ruby/stats"
+require "fsl-ruby/utils"
+
+module FSL
+
+end

data/lib/fsl-ruby/bet.rb

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+module FSL
+	class BET # bet <input> <output> [options]
+
+# Main bet2 options:
+	# -o generate brain surface outline overlaid onto original image
+	# -m generate binary brain mask
+	# -s generate rough skull image (not as clean as what betsurf generates)
+	# -n don't generate the default brain image output
+	# -f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
+	# -g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
+	# -r <r> head radius (mm not voxels); initial surface sphere is set to half of this
+	# -c < x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
+	# -t apply thresholding to segmented brain image and mask
+	# -e generates brain surface as mesh in .vtk format.
+		@@command_path = '/usr/local/fsl/bin/bet'
+
+			def self.command_path=(path)
+				@@command_path = path
+			end
+
+			def self.command_path
+				@@command_path
+			end
+
+
+		@@options_map = { outline: '-o',
+							mask: '-m',
+							skull: '-s',
+							no_output: '-n',
+							fi_threshold: '-f',
+							v_gradient: '-g',
+							radius: '-r',
+							centre: '-c',
+							thresholding: '-t',
+							mesh: '-e'
+						}
+
+		def initialize(input_file, output_dir, opt = {})
+			@input_file = input_file
+			@basename = File.basename(input_file, '.nii.gz')
+			@output_dir = output_dir
+			@opt = opt
+		end
+
+		def self.options_map
+			@@options_map
+		end
+
+		def map_vals(val)
+			if val == true || val == false
+				''
+			else
+				val.to_s
+			end
+		end
+
+		def map_options(opt ={})
+			opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
+		end
+
+		def argument_list
+			map_options(@opt).collect {|k,v| v}.join(' ')
+		end
+
+		def command
+			command_str = "#{self.class.command_path} #{@input_file} #{@output_dir}/#{@basename}_brain #{argument_list}"
+			puts "Running BET with command: #{command_str}..."
+			result = `#{command_str}`
+			exit_code = $?
+			case exit_code
+				when 0
+					puts "Done running BET."
+					return result
+				else
+					puts "An error ocurred while running BET"
+			        #   exit_error = Dcm2nii::Runner::UnexpectedExitError.new
+			        #   exit_error.exit_code = exit_code
+			        #   raise exit_error
+			        # end
+			end
+		end
+
+		def get_result
+  			return `find #{@output_dir} -name *_brain.nii*`.chomp
+		end
+
+	end
+end

data/lib/fsl-ruby/first.rb

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+module FSL
+	class FIRST
+
+# def first(bet_file, id, tmp_dir)
+#   `run_first_all -i #{bet_file} -b -s L_Hipp,R_Hipp -o #{tmp_dir}/#{id}`
+#   first_files = {}
+#   first_files[:origsegs] = `find #{tmp_dir} -name *origsegs.nii*`.chomp
+#   first_files[:firstseg] = `find #{tmp_dir} -name *firstseg.nii*`.chomp
+#   return first_files
+# end
+
+# Usage: run_first_all [options] -i <input_image> -o <output_image>
+
+# Optional arguments:
+#   -m <method>      : method must be one of auto, fast, none or a (numerical) threshold value
+#   -b               : input is already brain extracted
+#   -s <name>        : run only on one specified structure (e.g. L_Hipp) or a comma separated list (no spaces)
+#   -a <img2std.mat> : use affine matrix (do not re-run registration)
+#   -3               : use 3-stage affine registration (only currently for hippocampus)
+#   -d               : do not cleanup image output files (useful for debugging)
+#   -v               : verbose output
+#   -h               : display this help message
+
+# e.g.:  run_first_all -i im1 -o output_name
+
+		@@command_path = '/usr/local/fsl/bin/run_first_all'
+
+			def self.command_path=(path)
+				@@command_path = path
+			end
+
+			def self.command_path
+				@@command_path
+			end
+
+
+		@@options_map = {
+							method: '-m',
+							already_bet: '-b',
+							structure: '-s',
+							affine: '-a',
+							threestage: '-3',
+							no_cleanup: '-d',
+							verbose: '-v',
+							help: '-h'
+						}
+
+		def initialize(input_file, output_file, opt = {})
+			@input_file = input_file
+			@basename = File.basename(input_file, '.nii.gz')
+			@output_file = output_file
+			@output_dir = File.dirname(output_file)
+			@opt = opt
+		end
+
+		def self.options_map
+			@@options_map
+		end
+
+		def map_vals(val)
+			if val == true || val == false
+				''
+			else
+				val.to_s
+			end
+		end
+
+		def map_options(opt ={})
+			opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
+		end
+
+		def argument_list
+			map_options(@opt).collect {|k,v| v}.join(' ')
+		end
+
+		def command
+			command_str = "#{self.class.command_path} #{argument_list} -i #{@input_file} -o #{@output_file}"
+			puts "Running FIRST with command: #{command_str}..."
+			result = `#{command_str}`
+			exit_code = $?
+			case exit_code
+				when 0
+					puts "Done running FIRST."
+					return result
+				else
+					puts "An error ocurred while running FIRST"
+			        #   exit_error = Dcm2nii::Runner::UnexpectedExitError.new
+			        #   exit_error.exit_code = exit_code
+			        #   raise exit_error
+			        # end
+			end
+		end
+
+		def get_result
+			first_files = {}
+			first_files[:origsegs] = `find #{@output_dir} -name *origsegs.nii*`.chomp
+			first_files[:firstseg] = `find #{@output_dir} -name *firstseg.nii*`.chomp
+			return first_files
+		end
+
+	end
+end

data/lib/fsl-ruby/stats.rb

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+module FSL
+	class Stats
+
+# Usage: fslstats [-t] <input> [options]
+
+# -t will give a separate output line for each 3D volume of a 4D timeseries
+# Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean
+
+# -l <lthresh> : set lower threshold
+# -u <uthresh> : set upper threshold
+# -r           : output <robust min intensity> <robust max intensity>
+# -R           : output <min intensity> <max intensity>
+# -e           : output mean entropy ; mean(-i*ln(i))
+# -E           : output mean entropy (of nonzero voxels)
+# -v           : output <voxels> <volume>
+# -V           : output <voxels> <volume> (for nonzero voxels)
+# -m           : output mean
+# -M           : output mean (for nonzero voxels)
+# -s           : output standard deviation
+# -S           : output standard deviation (for nonzero voxels)
+# -w           : output smallest ROI <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> containing nonzero voxels
+# -x           : output co-ordinates of maximum voxel
+# -X           : output co-ordinates of minimum voxel
+# -c           : output centre-of-gravity (cog) in mm coordinates
+# -C           : output centre-of-gravity (cog) in voxel coordinates
+# -p <n>       : output nth percentile (n between 0 and 100)
+# -P <n>       : output nth percentile (for nonzero voxels)
+# -a           : use absolute values of all image intensities
+# -n           : treat NaN or Inf as zero for subsequent stats
+# -k <mask>    : use the specified image (filename) for masking - overrides lower and upper thresholds
+# -h <nbins>   : output a histogram (for the thresholded/masked voxels only) with nbins
+# -H <nbins> <min> <max>   : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max
+
+# Note - thresholds are not inclusive ie lthresh<allowed<uthresh
+
+		@@command_path = '/usr/local/fsl/bin/fslstats'
+
+			def self.command_path=(path)
+				@@command_path = path
+			end
+
+			def self.command_path
+				@@command_path
+			end
+
+@@options_map = {
+					low_threshold: '-l', # <lthresh> : set lower threshold
+					up_threshold: '-u', # <uthresh> : set upper threshold
+					robust_intensity: '-r', # output <robust min intensity> <robust max intensity>
+					intensity: '-R', # output <min intensity> <max intensity>
+					entropy: '-e', # output mean entropy ; mean(-i*ln(i))
+					entropy_nonzero: '-E',# output mean entropy (of nonzero voxels)
+					voxels: '-v', # output <voxels> <volume>
+					voxels_nonzero: '-V', # output <voxels> <volume> (for nonzero voxels)
+					mean: '-m', # output mean
+					mean_nonzero: '-M',# output mean (for nonzero voxels)
+					stdev: '-s', # output standard deviation
+					stdev_nonzero: '-S', # output standard deviation (for nonzero voxels)
+					smallest_roi: '-w', # output smallest ROI <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> containing nonzero voxels
+					coord_maxvoxel: '-x', # output co-ordinates of maximum voxel
+					coord_minvoxel: '-X', # output co-ordinates of minimum voxel
+					cog_mm: '-c', # output centre-of-gravity (cog) in mm coordinates
+					cog_voxel: '-C', # output centre-of-gravity (cog) in voxel coordinates
+					nth_percentile: '-p', # <n> output nth percentile (n between 0 and 100)
+					nth_percentage_nonzero: '-P', # <n> output nth percentile (for nonzero voxels)
+					abs: '-a', # use absolute values of all image intensities
+					nan_as_zero: '-n', # treat NaN or Inf as zero for subsequent stats
+					mask: '-k', #<mask> use the specified image (filename) for masking - overrides lower and upper thresholds
+					hist: '-h', #<nbins> output a histogram (for the thresholded/masked voxels only) with nbins
+					hist_minmax: '-H' # <nbins> <min> <max>   : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max
+					}
+
+		def initialize(input_file, separate=false, opt = {})
+			@input_file = input_file
+			@basename = File.basename(input_file, '.nii.gz')
+			@separate = separate
+			@opt = opt
+		end
+
+		def self.options_map
+			@@options_map
+		end
+
+		def map_vals(val)
+			if val == true || val == false
+				''
+			else
+				val.to_s
+			end
+		end
+
+		def map_options(opt ={})
+			opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
+		end
+
+		def argument_list
+			map_options(@opt).collect {|k,v| v}.join(' ')
+		end
+
+		def command
+			sf = @separate ? '-t' : ''
+			command_str = "#{self.class.command_path} #{sf} #{@input_file} #{argument_list}"
+			puts "Running FSLSTATS with command: #{command_str}..."
+			result = `#{command_str}`
+			exit_code = $?
+			case exit_code
+				when 0
+					puts "Done running FSLSTATS."
+					return result
+				else
+					puts "An error ocurred while running FSLSTATS"
+			        #   exit_error = Dcm2nii::Runner::UnexpectedExitError.new
+			        #   exit_error.exit_code = exit_code
+			        #   raise exit_error
+			        # end
+			end
+		end
+
+		def get_result
+  			# return `find #{@output_dir} -name *_brain.nii*`.chomp
+		end
+
+	end
+end

data/lib/fsl-ruby/utils.rb

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+module FSL
+	class UTILS # Misc FSL utilities grouped under FSLUTILS
+
+		@@FSLHOME= '/usr/local/fsl/bin/'
+
+		def self.roi(input, output, xmin, xsize, ymin, ysize, zmin, zsize)
+		# Usage: 	fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
+		#        		fslroi <input> <output> <tmin> <tsize>
+		#        		fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
+		# Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension.
+			command_str = "#{@@FSLHOME}/fslroi #{input} #{output} #{xmin.to_s} #{xsize.to_s} #{ymin.to_s} #{ysize.to_s} #{zmin.to_s} #{zsize.to_s}"
+			puts "Running FSLROI with command #{command_str}..."
+			result = `#{command_str}`
+			puts "Done running FSLROI."
+		end
+
+		def self.swapdim(input,axes,output)
+		# Usage: fslswapdim <input> <a> <b> <c> [output]
+
+		#   where a,b,c represent the new x,y,z axes in terms of the old axes.  They can take values of -x,x,y,-y,z,-z
+		#   or RL,LR,AP,PA,SI,IS (in the case of nifti inputs)  e.g.  fslswapdim invol y x -z outvol
+		#   or  fslswapdim invol RL PA IS outvol where the latter will convert to axial slicing  (to match the avg152 images)
+			command_str = "#{@@FSLHOME}/fslswapdim #{input} #{axes} #{output}"
+			puts "Running FSLSWAPDIM with command #{command_str}..."
+			result = `#{command_str}`
+			puts "Done running FSLSWAPDIM."
+		end
+
+	end
+end

data/lib/fsl-ruby/version.rb

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+module FSL
+    VERSION = "0.0.1"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: fsl-ruby
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Simon Rascovsky
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-11-21 00:00:00.000000000 Z
+dependencies: []
+description: Ruby Wrapper for the FSL Neuroimaging suite
+email:
+- simonmd@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .DS_Store
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- fsl-ruby.gemspec
+- lib/.DS_Store
+- lib/fsl-ruby.rb
+- lib/fsl-ruby/bet.rb
+- lib/fsl-ruby/first.rb
+- lib/fsl-ruby/stats.rb
+- lib/fsl-ruby/utils.rb
+- lib/fsl-ruby/version.rb
+homepage: ''
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Ruby Wrapper for the FSL Neuroimaging suite
+test_files: []