Class: FSL::UTILS

Inherits:
Object
  • Object
show all
Defined in:
lib/fsl-ruby/utils.rb

Overview

Misc FSL utilities grouped under FSLUTILS

Constant Summary collapse

@@FSLHOME = 
'/usr/local/fsl/bin/'

Class Method Summary collapse

Class Method Details

.roi(input, output, xmin, xsize, ymin, ysize, zmin, zsize) ⇒ Object 



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# File 'lib/fsl-ruby/utils.rb', line 6

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

.swapdim(input, axes, output) ⇒ Object 



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# File 'lib/fsl-ruby/utils.rb', line 17

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