Package gov.nih.mipav.model.file

Class FileMGH

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileMGH
public class FileMGH extends FileBase
The class reads MGH files. The 4 by 4 matrix in MGH transforms x,y,z indexes to (right, anterior, superior) coordinates where +x = Right, +y = Anterior, +z = Superior. In MIPAV the 4 by 4 matrix does not imply the axis orientations.

The MGH definition is: [right] = [xr yr zr] [ xsize * x] + [rorigin] [anterior] = [xa ya za] [ ysize * y] + [aorigin] [superior] = [xs ys zs] [ zsize * z] + [sorigin] Now in going to MIPAV a change must occur. MGH has L->R and P->A while MIPAV uses R->L in all axes and A->P in axes 0 and 1 and P->A in axis 2, so this would cause xr, yr, zr, rorigin, xa, ya, za, and aorigin to be multiplied by -1. cr, ca, and cs refer to the center point of the scanner coordinate system.

A 284 byte header always precedes the data buffer In version 1 if the goodRASFlag invalid input: '<'= 0, then only the first 30 bytes are read. If the goodRASFlag > 0, then the first 90 bytes are read

Immediately after the data buffer other optional data structures may be found: They are: Recovery time in milliseconds float Flip angle in radians float Echo time in milliseconds float Inversion time in millseconds float Field of view in millimeters float Comment about fov field from Nick Schmansky: The FoV field should be ignored. In discussing this field with Bruce Fischl, and looking more closely at the code, it appears to be a field with a long and inconsistent usage history (in how it is set and where the data originates). We do not rely on it in our binaries. Lastly, tags including the Talairach transform file name and a list of commands used to create this data(provenance info) may be present.

I am not reading the contents of the Talairach transform file for 3 reasons: 1.) This information is probably not very useful. 2.) Every sample file that I obtained from MGH gave the same name: talairach.xfm. If this name is always used, then it is impossible to tell which .mgh file it corresponds to. 3.) The Talairach transform file is a clear ascii file, so it can be easily read with any number of common programs.

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  • Field Details

    • MRI_UCHAR

      private static final int MRI_UCHAR
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    • MRI_INT

      private static final int MRI_INT
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    • MRI_LONG

      private static final int MRI_LONG
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    • MRI_FLOAT

      private static final int MRI_FLOAT
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    • MRI_SHORT

      private static final int MRI_SHORT
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    • MRI_BITMAP

      private static final int MRI_BITMAP
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    • MRI_TENSOR

      private static final int MRI_TENSOR
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    • TAG_OLD_COLORTABLE

      private static final int TAG_OLD_COLORTABLE
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    • TAG_OLD_USEREALRAS

      private static final int TAG_OLD_USEREALRAS
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    • TAG_CMDLINE

      private static final int TAG_CMDLINE
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    • TAG_OLD_SURF_GEOM

      private static final int TAG_OLD_SURF_GEOM
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    • TAG_OLD_MGH_XFORM

      private static final int TAG_OLD_MGH_XFORM
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    • TAG_MGH_XFORM

      private static final int TAG_MGH_XFORM
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    • MAX_CMDS

      private static final int MAX_CMDS
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    • cmdlines

      String[] cmdlines
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    • ncmds

      int ncmds
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    • axisOrientation

      private int[] axisOrientation
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    • bytesPerValue

      private int bytesPerValue
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    • ca

      private float ca
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    • cr

      private float cr
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    • cs

      private float cs
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    • dataType

      private int dataType
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    • depth

      private int depth
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    • dof

      private int dof
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    • extents

      private int[] extents
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    • file

      private File file
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    • fileDir

      private String fileDir
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    • fileInfo

      private FileInfoMGH fileInfo
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    • fileLength

      private long fileLength
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    • fileName

      private String fileName
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    • fis

      private FileInputStream fis
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    • flipAngle

      private float flipAngle
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    • fov

      private float fov
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    • goodRASFlag

      private short goodRASFlag
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    • gunzip

      private boolean gunzip
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    • height

      private int height
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    • image

      private ModelImage image
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    • matrix

      private TransMatrix matrix
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    • mghType

      private int mghType
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    • nFrames

      private int nFrames
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    • optionalStructuresLocation

      private long optionalStructuresLocation
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    • origin

      private float[] origin
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    • resolutions

      private float[] resolutions
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    • te

      private float te
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    • ti

      private float ti
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    • tr

      private float tr
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    • version

      private int version
      Present version number is 1.

    • width

      private int width
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    • xa

      private float xa
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    • xr

      private float xr
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    • xs

      private float xs
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    • ya

      private float ya
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    • yr

      private float yr
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    • ys

      private float ys
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    • za

      private float za
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    • zr

      private float zr
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    • zs

      private float zs
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  • Constructor Details

    • FileMGH

      public FileMGH(String fName, String fDir)
      Constructs new file object.
      Parameters:
      fName - File name.
      fDir - File directory.

  • Method Details

    • finalize

      public void finalize()
      Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
      Overrides:
      finalize in class FileBase

    • getFileInfo

      public FileInfoMGH getFileInfo()
      Returns the FileInfoMGH read from the file.
      Returns:
      File info read from file, or null if it has not been read.

    • readHeader

      public boolean readHeader(String imageFileName, String fileDir) throws IOException
      Reads the MGH header and stores the information in fileInfo.
      Parameters:
      imageFileName - File name of image.
      fileDir - Directory.
      Returns:
      Flag to confirm a successful read.
      Throws:
      IOException - if there is an error reading the header
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    • readImage

      public ModelImage readImage(boolean one) throws IOException, OutOfMemoryError
      Reads a MGH image file by reading the header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.
      Parameters:
      one - flag indicating one image of a 3D dataset should be read in.
      Returns:
      The image.
      Throws:
      IOException - if there is an error reading the file
      OutOfMemoryError
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    • readImage

      public void readImage(float[] buffer) throws IOException, OutOfMemoryError
      Reads a MGH image file by reading the header then making a FileRaw to read the file. Image data is left in buffer. If the fileInfo cannot be found, the header will be located and read first. Image is not 'flipped', and neither units of measure nor orientation are set.
      Parameters:
      buffer - Image buffer to store image data into.
      Throws:
      IOException - if there is an error reading the file
      OutOfMemoryError
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    • writeImage

      public void writeImage(ModelImage image, FileWriteOptions options) throws IOException
      Writes a MGH or MGZ format type image.
      Parameters:
      image - Image model of data to write.
      options - options such as starting and ending slices and times
      Throws:
      IOException - if there is an error writing the file

    • attachFileInfo

      private void attachFileInfo(FileInfoMGH fileInfo, ModelImage image)
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      Parameters:
      fileInfo - -- a NIFTI file Info that has already been read
      image - -- a ModelImage that the fileInfo needs to be attached to

    • getAxisOrientation

      public static int[] getAxisOrientation(TransMatrix mat)
      Return the 3 axis orientation codes that correspond to the closest standard anatomical orientation of the (i,j,k) axes.
      Parameters:
      mat - 4x4 matrix that transforms (i,j,k) indexes to x,y,z coordinates where +x =Left, +y = Posterior, +z = Superior Only the upper-left 3x3 corner of the matrix is used This routine finds the permutation of (x,y,z) which has the smallest angle to the (i,j,k) axes directions, which are columns of the input matrix Errors: The codes returned will be zero.
      Returns:
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    • getOffset

      private int getOffset()
      Helper method to calculate the offset for getting only the middle NIFTI image slice from the 3D file.
      Returns:
      offset

    • updateorigins

      private void updateorigins(FileInfoBase[] fileInfo)
      Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
      Parameters:
      fileInfo - DOCUMENT ME!