fsl-ruby 0.0.1
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- data/.DS_Store +0 -0
- data/.gitignore +17 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +1 -0
- data/fsl-ruby.gemspec +19 -0
- data/lib/.DS_Store +0 -0
- data/lib/fsl-ruby.rb +9 -0
- data/lib/fsl-ruby/bet.rb +88 -0
- data/lib/fsl-ruby/first.rb +102 -0
- data/lib/fsl-ruby/stats.rb +124 -0
- data/lib/fsl-ruby/utils.rb +30 -0
- data/lib/fsl-ruby/version.rb +3 -0
- metadata +59 -0
data/.DS_Store
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2012 Simon Rascovsky
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# Fsl::Ruby
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A Ruby wrapper for the FSL neuroimaging suite
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## Installation
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Add this line to your application's Gemfile:
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gem 'fsl-ruby'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install fsl-ruby
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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require "bundler/gem_tasks"
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# -*- encoding: utf-8 -*-
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'fsl-ruby/version'
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Gem::Specification.new do |gem|
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gem.name = "fsl-ruby"
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gem.version = FSL::VERSION
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gem.authors = ["Simon Rascovsky"]
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gem.email = ["simonmd@gmail.com"]
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gem.description = %q{Ruby Wrapper for the FSL Neuroimaging suite}
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gem.summary = %q{Ruby Wrapper for the FSL Neuroimaging suite}
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gem.homepage = ""
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gem.files = `git ls-files`.split($/)
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gem.executables = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
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gem.test_files = gem.files.grep(%r{^(test|spec|features)/})
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gem.require_paths = ["lib"]
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end
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data/lib/.DS_Store
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data/lib/fsl-ruby.rb
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data/lib/fsl-ruby/bet.rb
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module FSL
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class BET # bet <input> <output> [options]
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# Main bet2 options:
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# -o generate brain surface outline overlaid onto original image
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# -m generate binary brain mask
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# -s generate rough skull image (not as clean as what betsurf generates)
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# -n don't generate the default brain image output
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# -f <f> fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
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# -g <g> vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
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# -r <r> head radius (mm not voxels); initial surface sphere is set to half of this
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# -c < x y z> centre-of-gravity (voxels not mm) of initial mesh surface.
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# -t apply thresholding to segmented brain image and mask
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# -e generates brain surface as mesh in .vtk format.
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@@command_path = '/usr/local/fsl/bin/bet'
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def self.command_path=(path)
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@@command_path = path
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end
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def self.command_path
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@@command_path
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end
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@@options_map = { outline: '-o',
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mask: '-m',
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skull: '-s',
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no_output: '-n',
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fi_threshold: '-f',
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v_gradient: '-g',
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radius: '-r',
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centre: '-c',
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thresholding: '-t',
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mesh: '-e'
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}
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def initialize(input_file, output_dir, opt = {})
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@input_file = input_file
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@basename = File.basename(input_file, '.nii.gz')
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@output_dir = output_dir
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@opt = opt
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end
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def self.options_map
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@@options_map
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end
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def map_vals(val)
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if val == true || val == false
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''
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else
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val.to_s
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end
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end
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def map_options(opt ={})
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opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
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end
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def argument_list
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map_options(@opt).collect {|k,v| v}.join(' ')
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end
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def command
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command_str = "#{self.class.command_path} #{@input_file} #{@output_dir}/#{@basename}_brain #{argument_list}"
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puts "Running BET with command: #{command_str}..."
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result = `#{command_str}`
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exit_code = $?
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case exit_code
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when 0
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puts "Done running BET."
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return result
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else
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puts "An error ocurred while running BET"
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# exit_error = Dcm2nii::Runner::UnexpectedExitError.new
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# exit_error.exit_code = exit_code
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# raise exit_error
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# end
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end
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end
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def get_result
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return `find #{@output_dir} -name *_brain.nii*`.chomp
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end
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end
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end
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module FSL
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class FIRST
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# def first(bet_file, id, tmp_dir)
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# `run_first_all -i #{bet_file} -b -s L_Hipp,R_Hipp -o #{tmp_dir}/#{id}`
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# first_files = {}
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# first_files[:origsegs] = `find #{tmp_dir} -name *origsegs.nii*`.chomp
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# first_files[:firstseg] = `find #{tmp_dir} -name *firstseg.nii*`.chomp
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# return first_files
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# end
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# Usage: run_first_all [options] -i <input_image> -o <output_image>
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# Optional arguments:
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# -m <method> : method must be one of auto, fast, none or a (numerical) threshold value
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# -b : input is already brain extracted
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# -s <name> : run only on one specified structure (e.g. L_Hipp) or a comma separated list (no spaces)
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# -a <img2std.mat> : use affine matrix (do not re-run registration)
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# -3 : use 3-stage affine registration (only currently for hippocampus)
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# -d : do not cleanup image output files (useful for debugging)
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# -v : verbose output
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# -h : display this help message
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# e.g.: run_first_all -i im1 -o output_name
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@@command_path = '/usr/local/fsl/bin/run_first_all'
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def self.command_path=(path)
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@@command_path = path
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end
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def self.command_path
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@@command_path
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end
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@@options_map = {
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method: '-m',
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already_bet: '-b',
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structure: '-s',
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affine: '-a',
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threestage: '-3',
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no_cleanup: '-d',
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verbose: '-v',
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help: '-h'
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}
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def initialize(input_file, output_file, opt = {})
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@input_file = input_file
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@basename = File.basename(input_file, '.nii.gz')
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@output_file = output_file
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@output_dir = File.dirname(output_file)
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@opt = opt
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end
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def self.options_map
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@@options_map
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end
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def map_vals(val)
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if val == true || val == false
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''
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else
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val.to_s
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end
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end
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def map_options(opt ={})
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opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
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end
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def argument_list
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map_options(@opt).collect {|k,v| v}.join(' ')
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end
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def command
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command_str = "#{self.class.command_path} #{argument_list} -i #{@input_file} -o #{@output_file}"
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puts "Running FIRST with command: #{command_str}..."
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result = `#{command_str}`
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exit_code = $?
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case exit_code
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when 0
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puts "Done running FIRST."
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return result
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else
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puts "An error ocurred while running FIRST"
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# exit_error = Dcm2nii::Runner::UnexpectedExitError.new
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# exit_error.exit_code = exit_code
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# raise exit_error
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# end
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end
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end
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def get_result
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first_files = {}
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first_files[:origsegs] = `find #{@output_dir} -name *origsegs.nii*`.chomp
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first_files[:firstseg] = `find #{@output_dir} -name *firstseg.nii*`.chomp
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return first_files
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end
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end
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end
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module FSL
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class Stats
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# Usage: fslstats [-t] <input> [options]
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# -t will give a separate output line for each 3D volume of a 4D timeseries
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# 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
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# -l <lthresh> : set lower threshold
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# -u <uthresh> : set upper threshold
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# -r : output <robust min intensity> <robust max intensity>
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# -R : output <min intensity> <max intensity>
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# -e : output mean entropy ; mean(-i*ln(i))
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# -E : output mean entropy (of nonzero voxels)
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# -v : output <voxels> <volume>
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# -V : output <voxels> <volume> (for nonzero voxels)
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# -m : output mean
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# -M : output mean (for nonzero voxels)
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# -s : output standard deviation
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# -S : output standard deviation (for nonzero voxels)
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# -w : output smallest ROI <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> containing nonzero voxels
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# -x : output co-ordinates of maximum voxel
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# -X : output co-ordinates of minimum voxel
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# -c : output centre-of-gravity (cog) in mm coordinates
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# -C : output centre-of-gravity (cog) in voxel coordinates
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# -p <n> : output nth percentile (n between 0 and 100)
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# -P <n> : output nth percentile (for nonzero voxels)
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# -a : use absolute values of all image intensities
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# -n : treat NaN or Inf as zero for subsequent stats
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# -k <mask> : use the specified image (filename) for masking - overrides lower and upper thresholds
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# -h <nbins> : output a histogram (for the thresholded/masked voxels only) with nbins
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# -H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max
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# Note - thresholds are not inclusive ie lthresh<allowed<uthresh
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@@command_path = '/usr/local/fsl/bin/fslstats'
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def self.command_path=(path)
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@@command_path = path
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end
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def self.command_path
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@@command_path
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end
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@@options_map = {
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low_threshold: '-l', # <lthresh> : set lower threshold
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up_threshold: '-u', # <uthresh> : set upper threshold
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robust_intensity: '-r', # output <robust min intensity> <robust max intensity>
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intensity: '-R', # output <min intensity> <max intensity>
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entropy: '-e', # output mean entropy ; mean(-i*ln(i))
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entropy_nonzero: '-E',# output mean entropy (of nonzero voxels)
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voxels: '-v', # output <voxels> <volume>
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voxels_nonzero: '-V', # output <voxels> <volume> (for nonzero voxels)
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mean: '-m', # output mean
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mean_nonzero: '-M',# output mean (for nonzero voxels)
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stdev: '-s', # output standard deviation
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stdev_nonzero: '-S', # output standard deviation (for nonzero voxels)
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smallest_roi: '-w', # output smallest ROI <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> containing nonzero voxels
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coord_maxvoxel: '-x', # output co-ordinates of maximum voxel
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coord_minvoxel: '-X', # output co-ordinates of minimum voxel
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cog_mm: '-c', # output centre-of-gravity (cog) in mm coordinates
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cog_voxel: '-C', # output centre-of-gravity (cog) in voxel coordinates
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nth_percentile: '-p', # <n> output nth percentile (n between 0 and 100)
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nth_percentage_nonzero: '-P', # <n> output nth percentile (for nonzero voxels)
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abs: '-a', # use absolute values of all image intensities
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nan_as_zero: '-n', # treat NaN or Inf as zero for subsequent stats
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mask: '-k', #<mask> use the specified image (filename) for masking - overrides lower and upper thresholds
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hist: '-h', #<nbins> output a histogram (for the thresholded/masked voxels only) with nbins
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hist_minmax: '-H' # <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max
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}
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def initialize(input_file, separate=false, opt = {})
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|
+
@input_file = input_file
|
75
|
+
@basename = File.basename(input_file, '.nii.gz')
|
76
|
+
@separate = separate
|
77
|
+
@opt = opt
|
78
|
+
end
|
79
|
+
|
80
|
+
def self.options_map
|
81
|
+
@@options_map
|
82
|
+
end
|
83
|
+
|
84
|
+
def map_vals(val)
|
85
|
+
if val == true || val == false
|
86
|
+
''
|
87
|
+
else
|
88
|
+
val.to_s
|
89
|
+
end
|
90
|
+
end
|
91
|
+
|
92
|
+
def map_options(opt ={})
|
93
|
+
opt.inject({}) { |h, (k, v)| h[k] = (self.class.options_map[k] + ' ' + map_vals(v)); h }
|
94
|
+
end
|
95
|
+
|
96
|
+
def argument_list
|
97
|
+
map_options(@opt).collect {|k,v| v}.join(' ')
|
98
|
+
end
|
99
|
+
|
100
|
+
def command
|
101
|
+
sf = @separate ? '-t' : ''
|
102
|
+
command_str = "#{self.class.command_path} #{sf} #{@input_file} #{argument_list}"
|
103
|
+
puts "Running FSLSTATS with command: #{command_str}..."
|
104
|
+
result = `#{command_str}`
|
105
|
+
exit_code = $?
|
106
|
+
case exit_code
|
107
|
+
when 0
|
108
|
+
puts "Done running FSLSTATS."
|
109
|
+
return result
|
110
|
+
else
|
111
|
+
puts "An error ocurred while running FSLSTATS"
|
112
|
+
# exit_error = Dcm2nii::Runner::UnexpectedExitError.new
|
113
|
+
# exit_error.exit_code = exit_code
|
114
|
+
# raise exit_error
|
115
|
+
# end
|
116
|
+
end
|
117
|
+
end
|
118
|
+
|
119
|
+
def get_result
|
120
|
+
# return `find #{@output_dir} -name *_brain.nii*`.chomp
|
121
|
+
end
|
122
|
+
|
123
|
+
end
|
124
|
+
end
|
@@ -0,0 +1,30 @@
|
|
1
|
+
module FSL
|
2
|
+
class UTILS # Misc FSL utilities grouped under FSLUTILS
|
3
|
+
|
4
|
+
@@FSLHOME= '/usr/local/fsl/bin/'
|
5
|
+
|
6
|
+
def self.roi(input, output, xmin, xsize, ymin, ysize, zmin, zsize)
|
7
|
+
# Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
|
8
|
+
# fslroi <input> <output> <tmin> <tsize>
|
9
|
+
# fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize>
|
10
|
+
# 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.
|
11
|
+
command_str = "#{@@FSLHOME}/fslroi #{input} #{output} #{xmin.to_s} #{xsize.to_s} #{ymin.to_s} #{ysize.to_s} #{zmin.to_s} #{zsize.to_s}"
|
12
|
+
puts "Running FSLROI with command #{command_str}..."
|
13
|
+
result = `#{command_str}`
|
14
|
+
puts "Done running FSLROI."
|
15
|
+
end
|
16
|
+
|
17
|
+
def self.swapdim(input,axes,output)
|
18
|
+
# Usage: fslswapdim <input> <a> <b> <c> [output]
|
19
|
+
|
20
|
+
# 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
|
21
|
+
# or RL,LR,AP,PA,SI,IS (in the case of nifti inputs) e.g. fslswapdim invol y x -z outvol
|
22
|
+
# or fslswapdim invol RL PA IS outvol where the latter will convert to axial slicing (to match the avg152 images)
|
23
|
+
command_str = "#{@@FSLHOME}/fslswapdim #{input} #{axes} #{output}"
|
24
|
+
puts "Running FSLSWAPDIM with command #{command_str}..."
|
25
|
+
result = `#{command_str}`
|
26
|
+
puts "Done running FSLSWAPDIM."
|
27
|
+
end
|
28
|
+
|
29
|
+
end
|
30
|
+
end
|
metadata
ADDED
@@ -0,0 +1,59 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: fsl-ruby
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
prerelease:
|
6
|
+
platform: ruby
|
7
|
+
authors:
|
8
|
+
- Simon Rascovsky
|
9
|
+
autorequire:
|
10
|
+
bindir: bin
|
11
|
+
cert_chain: []
|
12
|
+
date: 2012-11-21 00:00:00.000000000 Z
|
13
|
+
dependencies: []
|
14
|
+
description: Ruby Wrapper for the FSL Neuroimaging suite
|
15
|
+
email:
|
16
|
+
- simonmd@gmail.com
|
17
|
+
executables: []
|
18
|
+
extensions: []
|
19
|
+
extra_rdoc_files: []
|
20
|
+
files:
|
21
|
+
- .DS_Store
|
22
|
+
- .gitignore
|
23
|
+
- Gemfile
|
24
|
+
- LICENSE.txt
|
25
|
+
- README.md
|
26
|
+
- Rakefile
|
27
|
+
- fsl-ruby.gemspec
|
28
|
+
- lib/.DS_Store
|
29
|
+
- lib/fsl-ruby.rb
|
30
|
+
- lib/fsl-ruby/bet.rb
|
31
|
+
- lib/fsl-ruby/first.rb
|
32
|
+
- lib/fsl-ruby/stats.rb
|
33
|
+
- lib/fsl-ruby/utils.rb
|
34
|
+
- lib/fsl-ruby/version.rb
|
35
|
+
homepage: ''
|
36
|
+
licenses: []
|
37
|
+
post_install_message:
|
38
|
+
rdoc_options: []
|
39
|
+
require_paths:
|
40
|
+
- lib
|
41
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
42
|
+
none: false
|
43
|
+
requirements:
|
44
|
+
- - ! '>='
|
45
|
+
- !ruby/object:Gem::Version
|
46
|
+
version: '0'
|
47
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
48
|
+
none: false
|
49
|
+
requirements:
|
50
|
+
- - ! '>='
|
51
|
+
- !ruby/object:Gem::Version
|
52
|
+
version: '0'
|
53
|
+
requirements: []
|
54
|
+
rubyforge_project:
|
55
|
+
rubygems_version: 1.8.23
|
56
|
+
signing_key:
|
57
|
+
specification_version: 3
|
58
|
+
summary: Ruby Wrapper for the FSL Neuroimaging suite
|
59
|
+
test_files: []
|