CNifti

Currently under development and not realeased yet! But should be ready for reading NIfTI image and header

CNifti is a wrapper for the standard C NIfTI 1 library found at http://afni.nimh.nih.gov/pub/dist/src/nifti/

Installation

Add this line to your application's Gemfile (not working before release):

gem 'c_nifti'

And then execute:

$ bundle

Or install it yourself as (not working before release):

$ gem install c_nifti

Usage

img = CNifti::Image.new(dimensions: [3,3,3,6], datatype: CNifti::HeaderElement::Datatype::UnsignedInt)

image_path = "image.nii.gz"
img = CNifti::Image.open(image_path)

img.header.ndim
img.header.nx
img.header.ny
img.header.nz
img.header.nt
img.header.nu
img.header.nv
img.header.nw
img.header.dim
img.header.nvox
img.header.nbyper
img.header.datatype
img.header.dx
img.header.dy
img.header.dz
img.header.dt
img.header.du
img.header.dv
img.header.dw
img.header.pixdim
img.header.scl_slope
img.header.scl_inter
img.header.cal_min
img.header.cal_max
img.header.qform_code
img.header.sform_code
img.header.freq_dim
img.header.phase_dim
img.header.slice_dim
img.header.slice_code
img.header.slice_start
img.header.slice_end
img.header.slice_duration
img.header.quatern_b
img.header.quatern_c
img.header.quatern_d
img.header.qoffset_x
img.header.qoffset_y
img.header.qoffset_z
img.header.qfac
img.header.qto_xyz
img.header.qto_ijk
img.header.sto_xyz
img.header.sto_ijk
img.header.toffset
img.header.xyz_units
img.header.time_units
img.header.nifti_type
img.header.intent_code
img.header.intent_p1
img.header.intent_p2
img.header.intent_p3
img.header.intent_name
img.header.descrip
img.header.aux_file
img.header.file_name
img.header.image_name
img.header.image_name_offset
img.header.swapsize
img.header.byteorder
img.header.analyze75_orient

img.header.description = "description"
img.header.aux_file = "aux_file"
img.header.file_name = "new_image.nii.gz" # resets the fname, iname and iname_offset of NIfTI

img.data.raw # returns the data into a unidimensional array
img.data.get_raw(0) # returns the data at index 0 from the unidimensional array
img.data.set_raw(0,1) # sets the data at index 0 from the unidimensional array to 1
img.data.shape # like img.header.dim but without the first element
img.data[0][0][0] # Supposing the data has 3 dimensions, returns its value
img.data[0][0][0] = 1 # Supposing the data has 3 dimensions, sets its value at position (0,0,0) to 1

img.save_as("out_#{image_path})

Not supported data types

• DT_COMPLEX
• DT_RGB
• DT_ALL
• DT_COMPLEX128
• DT_COMPLEX256
• DT_RGBA32

NIfTI extensions are not supported

Contributing

1. Fork it ( https://github.com/rafamanzo/c_nifti/fork )
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 a new Pull Request