Class: SeriesDescriptionParameters

Inherits:

Object

• Object
• SeriesDescriptionParameters

Defined in:

lib/metamri/series_description_parameters.rb

Overview

Provides a mapping between series descriptions that are extracted from raw image headers and some associated attributes.

Constant Summary

SERIES_DESCRIPTIONS =

:stopdoc:

{
  "3-P,Localizer" =>                  [ "3PlaneLoc", "anat", nil ],
  "gre field map rhrcctrl = 15" =>    [ "Fieldmap", "epan", nil ],
  "SAG EPI Test 1 2 3" =>             [ "EPITest", "epan", "sag" ],
  "3D IR AX T1 - NEW" =>              [ "T1_EFGRE3D", "anat", "ax" ],
  "AX T2 W FR FSE 1.7 skip 0.3" =>    [ "T2_FSE", "fse", "ax" ],
  "High Order Shim 28cm" =>           [ "Shim", "anat", nil ],
  "SAG gre field map rhrcctr =15" =>  [ "Fieldmap", "epan", "sag" ],
  "dti w/ card gate" =>               [ "DTI", "epan", nil ],
  "HOS Head coil" =>                  [ "3PlaneLoc", "anat", nil ],
  "Localizer" =>                      [ "3PlaneLoc", "anat", nil ],
  "F Map; rhrcctrl 15; te7, 10" =>    [ "Fieldmap", "epan", nil ],
  "SAG EPI TEST" =>                   [ "EPITest", "epan", "sag" ],
  "ASL CBF" =>                        [ "AlsopsASL", "anat", nil ],
  "DTI - prev 39 slices" =>           [ "DTI", "epan", nil ],
  "3D IR COR T1 - NEW" =>             [ "T1_EFGRE3D", "anat", "cor" ],
  "SAG T2 W FSE 1.7 skip 0.3" =>      [ "T2_FSE", "fse", "sag" ],
  "COR T2 W FSE 1.7 skip 0.3" =>      [ "T2_FSE", "fse", "cor" ],
  "3plane - hirez" =>                 [ "3PlaneLoc", "anat", nil ],
  "SAG gre field map rhrcctr =1?" =>  [ "Fieldmap", "epan", "sag" ],
  "SAG EPI Test 1 2 3" =>             [ "EPITest", "epan", "sag" ],
  "dti w/o card gate" =>              [ "DTI", "epan", nil ],
  "Ax Flair irFSE" =>                 [ "T1_Flair", "fse", "ax" ],
  "DTI" =>                            [ "DTI", "epan", nil ],
  "AX T2 Flair" =>                    [ "T2_Flair", "fse", "ax" ],
  "AX T2 FLAIR" =>                    [ "T2_Flair", "fse", "ax" ],
  "SAG EPI Snod" =>                   [ "fMRI_snod", "epan", "sag" ],
  "SAG EPI Resting" =>                [ "fMRI_rest", "epan", "sag" ],
  "SAG EPI Snod (141 x 2)" =>         [ "fMRI_snod", "epan", "sag" ],
  "DTI - 10 Dir 1.8mm" =>             [ "DTI", "epan", nil ],
  "F Map; rhrcctrl 15; te6, 9" =>     [ "Fieldmap", "epan", nil ],
  "ASSET CAL" =>                      [ "ASSET_Calibration", "epan", nil ],
  "SAG EPI Resting (180)" =>          [ "fMRI_rest", "epan", "sag" ],
  "Sag SMAPS" =>                      [ "smaps", "anat", "sag" ]
}

Instance Attribute Summary

• #acq_plane ⇒ Object readonly

  The scan acquisition plane: axial, coronal, or sagittal.

• #anat_type ⇒ Object readonly

  Used as an argument to to3d, the AFNI command used to reconstruct a collection of dicom files into a single nifti data set.

• #scan_type ⇒ Object readonly

  A string used to build nice file names for reconstructed data sets.

Instance Method Summary

• #initialize(series_description) ⇒ SeriesDescriptionParameters constructor

  Creates a new object based on a series description string.

Constructor Details

#initialize(series_description) ⇒ SeriesDescriptionParameters

Creates a new object based on a series description string. The series description for an image is conveniently available as an attribute of the RawImageFile class.

Note that the series descriptions inside image headers sometimes have trailing white space, the constructor here strips and chomps it. Be advised of this behavior.

sd = SeriesDescription.new('3D IR AX T1 - NEW')

sd.scan_type

=> "T1_EFGRE3D"

sd.anat_type

=> "anat"

sd.acq_plane

=> "axial"

Raises:

• (IndexError)

# File 'lib/metamri/series_description_parameters.rb', line 77

def initialize(series_description)
  @series_description = series_description.strip.chomp
  raise IndexError if not SERIES_DESCRIPTIONS.has_key?(@series_description)
  @scan_type, @anat_type, @acq_plane = SERIES_DESCRIPTIONS[@series_description]
end

Instance Attribute Details

#acq_plane ⇒ Object (readonly)

The scan acquisition plane: axial, coronal, or sagittal

# File 'lib/metamri/series_description_parameters.rb', line 53

def acq_plane
  @acq_plane
end

#anat_type ⇒ Object (readonly)

Used as an argument to to3d, the AFNI command used to reconstruct a collection of dicom files into a single nifti data set

# File 'lib/metamri/series_description_parameters.rb', line 50

def anat_type
  @anat_type
end

#scan_type ⇒ Object (readonly)

A string used to build nice file names for reconstructed data sets

# File 'lib/metamri/series_description_parameters.rb', line 46

def scan_type
  @scan_type
end