Package gov.nih.mipav.model.file

Class FileAfni

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileAfni
public class FileAfni extends FileBase
Afni file format.

In Afni 3 .HEAD files may be present with just 1 .BRIK file containing the original Data. The +orig.BRIK file will contain the data, the +orig.HEAD file will describe transformation to create the original image, the +acpc.HEAD file will describe the transformation needed to create the acpc image, and the +tlrc.HEAD file will describe the transformation needed to create the Talairach image.

Special notes:

The document README.attributes specifies DICOM order for MARKS_XYZ, but the sample file anat+orig.HEAD has dataset order. The sample file anat+ACPC.HEAD has DICOM order.

The original data must be resampled to cubic voxels for +acpc and +tlrc space. In FAQ 67, How can I compare 'small' and 'big' in Talairach box datasets, the text states:
If you have used the default 1 mm. voxel size in +tlrc coordinates(as almost everyone does)...

The function THD_3dmm_to_dicomm does changes the ordering of x, y, and z, but never inverts them. That is either R-L or L-R could be present in AFNI's Dicom ordering, either S-I or I-S could be present in AFNI's dicom ordering, and either A-P or P-A could be present in AFNI's dicom ordering. I perform inversions in my code so that I always have x = R-L, Y = A-P, and Z = I-S, the standard dicom ordering.

To obtain the afni rr, bvec, and svec values, I must not invert axes in dicom ordering, and I must not adjust the marker coordinates for resolution and origin.

The function of the SKIP fields is not defined in the AFNI documentation.

Note that AFNI code uses mfor for forward transformation and mbac for backward transformation. Our interpolation routines perform a output to input mapping so since I am skipping the transform() section of AlgorithmTransform which has the line xfrm = matrixtoInverseArray(transMatrix);
I wish to use mbac in FileAfni and ViewJFrameTriImage.
For +orig to +acpc mapping mbac is simply the transpose(also the inverse) of mfor.
For +acpc to +tlrc use 1 over the scale factors in mbac as opposed to the scale factors in mfor.

Note that in the sample files func+orig.head and anat+orig.head the origin location in millimeters is chosen so that 0,0,0 in millimeters is at the center of the image. In anat+acpc.head and anat+tlrc.head the origin location in millimeters ensures that the Talairach center is at 0,0,0.

AFNI:Software for Analysis and Visualization of Functional Magnetic Resonance Neuroimages by Robert W. Cox states: "In some applications, gaps are present between the functional slices. For example, some investigators using sagittal functional images do not collect data that spans the longitudinal fissure, but instead leave a 3-5 mm gap there. The auxiliary program abut can provide zero-filled images to fill in the gaps, and can resample the nonzero slices to a finer mesh if needed(e.g., to fill a 2 mm gap in a series of 4 mm functional slices). Resampling in the slice select direction between contiguous input slices can be done using nearest- neighbor, linear, or cubic interpolation, at the user's discretion. Interpolation is not done across the boundaries between the gap-filling zero images and the nonzero user-supplied images; that is, interpolation is only done inside spatially contiguous blocks of actual input data."

A second special consideration exists in the interpolation of functional data. The MCW AFNI - User Manual states: "In this version of AFNI, the threshold data (e.g., correlation coefficient) is always resampled using the nearest neighbor method. This is because thresholding with an interpolated nonlinear statistic is a somewhat dubious procedure." At another point the manual states: "Threshold data in functional datasets is always resampled using the nearest neighbor mode. This is becasue it is somewhat unreasonable to interpolate a nonlinear statistic (such as correlation coefficient) between voxels, and then to interpret this statistic using probabilistic models that assume independence."

v1:time+orig.HEAD has 1 = ORI_L2R_TYPE for the third ORIENT_SPECIFIC value, -53 for the third ORIGIN value, and 7 for the third delta value. However, delta should be negative for ORI_L2R_TYPE. I changed the values to those found in v2:time+orig.HEAD, namely 1 for the third ORIENT_SPECIFIC value, 52 for the third ORIGIN value, and -7 for the third delta value. The observed overlap was then excellent for v1_time+orig.HEAD and anat+orig.HEAD, anat+ACPC.HEAD, and anat+TLRC.HEAD.

Author:
William Gandler
See Also:

  • Field Details

    • INTEGER_ATTRIBUTE

      public static final int INTEGER_ATTRIBUTE
      attribute types.
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    • FLOAT_ATTRIBUTE

      public static final int FLOAT_ATTRIBUTE
      DOCUMENT ME!
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    • STRING_ATTRIBUTE

      public static final int STRING_ATTRIBUTE
      DOCUMENT ME!
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    • ANAT_SPGR_TYPE

      public static final int ANAT_SPGR_TYPE
      funcType for anatType == true.
      See Also:

    • ANAT_FSE_TYPE

      public static final int ANAT_FSE_TYPE
      DOCUMENT ME!
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    • ANAT_EPI_TYPE

      public static final int ANAT_EPI_TYPE
      DOCUMENT ME!
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    • ANAT_MRAN_TYPE

      public static final int ANAT_MRAN_TYPE
      DOCUMENT ME!
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    • ANAT_CT_TYPE

      public static final int ANAT_CT_TYPE
      DOCUMENT ME!
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    • ANAT_SPECT_TYPE

      public static final int ANAT_SPECT_TYPE
      DOCUMENT ME!
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    • ANAT_PET_TYPE

      public static final int ANAT_PET_TYPE
      DOCUMENT ME!
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    • ANAT_MRA_TYPE

      public static final int ANAT_MRA_TYPE
      DOCUMENT ME!
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    • ANAT_BMAP_TYPE

      public static final int ANAT_BMAP_TYPE
      DOCUMENT ME!
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    • ANAT_DIFF_TYPE

      public static final int ANAT_DIFF_TYPE
      DOCUMENT ME!
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    • ANAT_OMRI_TYPE

      public static final int ANAT_OMRI_TYPE
      DOCUMENT ME!
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    • ANAT_BUCK_TYPE

      public static final int ANAT_BUCK_TYPE
      DOCUMENT ME!
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    • FUNC_FIM_TYPE

      public static final int FUNC_FIM_TYPE
      funcType for anatType == false.
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    • FUNC_THR_TYPE

      public static final int FUNC_THR_TYPE
      DOCUMENT ME!
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    • FUNC_COR_TYPE

      public static final int FUNC_COR_TYPE
      DOCUMENT ME!
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    • FUNC_TT_TYPE

      public static final int FUNC_TT_TYPE
      DOCUMENT ME!
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    • FUNC_FT_TYPE

      public static final int FUNC_FT_TYPE
      DOCUMENT ME!
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    • FUNC_ZT_TYPE

      public static final int FUNC_ZT_TYPE
      DOCUMENT ME!
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    • FUNC_CT_TYPE

      public static final int FUNC_CT_TYPE
      DOCUMENT ME!
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    • FUNC_BT_TYPE

      public static final int FUNC_BT_TYPE
      DOCUMENT ME!
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    • FUNC_BN_TYPE

      public static final int FUNC_BN_TYPE
      DOCUMENT ME!
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    • FUNC_GT_TYPE

      public static final int FUNC_GT_TYPE
      DOCUMENT ME!
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    • FUNC_PT_TYPE

      public static final int FUNC_PT_TYPE
      DOCUMENT ME!
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    • FUNC_BUCK_TYPE

      public static final int FUNC_BUCK_TYPE
      DOCUMENT ME!
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    • FUNC_THR_SCALE_SHORT

      public static final float FUNC_THR_SCALE_SHORT
      Unfortunately, the func type codes overlap for Func and Anat datasets. This means that one cannot tell the contents of a dataset from a single attribute. Default scale factors for functional data threshold values stored as shorts If BRICK_FLOAT_FACS is not supplied and the threshold functional data is stored as shorts, then AFNI will apply a default scale factor unless the data is FUNC_FIM_TYPE with only an intensity value and no threshold value or FUNC_BUCK_TYPE which has a default scale factor of 1.
      See Also:

    • FUNC_COR_SCALE_SHORT

      public static final float FUNC_COR_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_TT_SCALE_SHORT

      public static final float FUNC_TT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_FT_SCALE_SHORT

      public static final float FUNC_FT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_ZT_SCALE_SHORT

      public static final float FUNC_ZT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_CT_SCALE_SHORT

      public static final float FUNC_CT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_BT_SCALE_SHORT

      public static final float FUNC_BT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_BN_SCALE_SHORT

      public static final float FUNC_BN_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_GT_SCALE_SHORT

      public static final float FUNC_GT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_PT_SCALE_SHORT

      public static final float FUNC_PT_SCALE_SHORT
      DOCUMENT ME!
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    • FUNC_THR_SCALE_BYTE

      public static final float FUNC_THR_SCALE_BYTE
      6 funcType of functional data have default scaling for byte data.
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    • FUNC_COR_SCALE_BYTE

      public static final float FUNC_COR_SCALE_BYTE
      DOCUMENT ME!
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    • FUNC_TT_SCALE_BYTE

      public static final float FUNC_TT_SCALE_BYTE
      DOCUMENT ME!
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    • FUNC_ZT_SCALE_BYTE

      public static final float FUNC_ZT_SCALE_BYTE
      DOCUMENT ME!
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    • FUNC_BT_SCALE_BYTE

      public static final float FUNC_BT_SCALE_BYTE
      DOCUMENT ME!
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    • FUNC_GT_SCALE_BYTE

      public static final float FUNC_GT_SCALE_BYTE
      DOCUMENT ME!
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    • MARKSET_ALIGN

      public static final int MARKSET_ALIGN
      marker types.
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    • MARKSET_BOUNDING

      public static final int MARKSET_BOUNDING
      DOCUMENT ME!
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    • WARP_AFFINE_TYPE

      public static final int WARP_AFFINE_TYPE
      warp types.
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    • WARP_TALAIRACH_12_TYPE

      public static final int WARP_TALAIRACH_12_TYPE
      DOCUMENT ME!
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    • UNITS_MSEC_TYPE

      public static final int UNITS_MSEC_TYPE
      time step units.
      See Also:

    • UNITS_SEC_TYPE

      public static final int UNITS_SEC_TYPE
      DOCUMENT ME!
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    • UNITS_HZ_TYPE

      public static final int UNITS_HZ_TYPE
      DOCUMENT ME!
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    • ATLAS_FRONT_TO_AC

      private static final float ATLAS_FRONT_TO_AC
      DOCUMENT ME!
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    • ATLAS_PC_TO_BACK

      private static final float ATLAS_PC_TO_BACK
      DOCUMENT ME!
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    • ATLAS_BOT_TO_AC

      private static final float ATLAS_BOT_TO_AC
      DOCUMENT ME!
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    • ATLAS_AC_TO_TOP

      private static final float ATLAS_AC_TO_TOP
      DOCUMENT ME!
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    • ATLAS_AC_TO_LAT

      private static final float ATLAS_AC_TO_LAT
      DOCUMENT ME!
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    • acpcAC

      private WildMagic.LibFoundation.Mathematics.Vector3f acpcAC
      Anterior Comissure in acpc space.

    • acpcMaxPt

      private WildMagic.LibFoundation.Mathematics.Vector3f acpcMaxPt
      DOCUMENT ME!

    • acpcMinPt

      private WildMagic.LibFoundation.Mathematics.Vector3f acpcMinPt
      DOCUMENT ME!

    • acpcName

      private String acpcName
      DOCUMENT ME!

    • acpcPC

      private WildMagic.LibFoundation.Mathematics.Vector3f acpcPC
      DOCUMENT ME!

    • acpcRes

      private float acpcRes
      DOCUMENT ME!

    • acquisitionDuration

      private float acquisitionDuration
      DOCUMENT ME!

    • alsoAcpc

      private boolean alsoAcpc
      DOCUMENT ME!

    • alsoOrig

      private boolean alsoOrig
      DOCUMENT ME!

    • anatomyParentnameString

      private String anatomyParentnameString
      DOCUMENT ME!

    • anatType

      private boolean anatType
      DOCUMENT ME!

    • anotherPtDicom

      private WildMagic.LibFoundation.Mathematics.Vector3f anotherPtDicom
      DOCUMENT ME!

    • brickFloatFacs

      private float[] brickFloatFacs
      DOCUMENT ME!

    • brickKeywordsString

      private String brickKeywordsString
      DOCUMENT ME!

    • brickLabsString

      private String[] brickLabsString
      Sub-brick names

    • brickStatAux

      private float[] brickStatAux
      Each BLT is defined by a struct that contains two 3x3 matrices and four 3-vectors (2*3*3 + 4*3 = the 30 numbers). These values are: [mfor] = 3x3 forward transformation matrix [0..8] 0,1,2 correspond to alpha.X, alpha.Y, alpha.Z 3,4,5 correspond to beta.X, beta.Y, beta.Z 6,7,8 correspond to gamma.X, gamma.Y, gamma.Z [mbac] = 3x3 backward transformation matrix [0..17] [bvec] = 3-vector for forward transformation [18..20] [svec] = 3-vector for backward transformation [21..23] [bot] [24..26] [top] [27..29] The matrices are stored in row major order; e.g., [ 0 1 2] [mfor] = [ 3 4 5] [ 6 7 8] the indices of the [mfor] matrix The forward transformation is [x_map] = [mfor][x_in] - [bvec] The backward transformation is [x_in] = [mbac][x_map] - [svec] which implies [svec] = -[mbac][bvec] and [mbac] = Inverse{[mfor]} The forward transformation is the transformation of Dicom order coordinates from the warp parent dataset (usually in the +orig view) to the warped dataset (usually +acpc or +tlrc). The backward transformation is just the inverse of the forward transformation, and is stored for convenience. It could be recomputed from the forward transformation whenever it was needed. The identity BLT would be stored as these 30 numbers: 1 0 0 0 1 0 [mfor] = I 0 0 1 1 0 0 0 1 0 [mbac] = I 0 0 1 0 0 0 [bvec] = 0 0 0 0 [svec] = 0 botx boty botz topx topy topz bot and top numbers depend on the application. If the transformation is WARP_TALAIRACH_TYPE, then each BLT type only applies to a bounded region of 3-space. The [bot] and [top] vectors define the limits for each BLT, in the warped [x_map] coordinates. These values are used in the function AFNI_transform_vector() to compute the transformation of a 3-vector between +orig and +tlrc coordinates. For example, to compute the transformation from +tlrc back to +orig of a vector [x_tlrc], the code must scan all 12 [bot]..[top] regions to see which BLT to use. Similarly, to transform [x_orig] from +orig to +tlrc, the vector must be transformed with each BLT and the result tested to see if it lies within the BLT's [bot]..[top] region. (if a lower bound is supposed to be -infinity, then that element of [bot] is -9999; if an upper bound is supposed to be +infinity then that element of [top] is +9999. For the +orig to +acpc transformation (of WARP_AFFINE_TYPE), the [bot] and [top] vectors store the bounding box of the transformed dataset. However, this fact isn't used much.

    • brickStats

      private float[] brickStats
      DOCUMENT ME!

    • brickType

      private int brickType
      DOCUMENT ME!

    • brickTypeNumber

      private int brickTypeNumber
      DOCUMENT ME!

    • brikDataType

      private int brikDataType
      DOCUMENT ME!

    • brikFileName

      private String brikFileName
      DOCUMENT ME!

    • bufferSize

      private int bufferSize
      DOCUMENT ME!

    • dataExtents

      private int[] dataExtents
      DOCUMENT ME!

    • dataOrient

      private int[] dataOrient
      DOCUMENT ME!

    • datasetKeywordsString

      private String datasetKeywordsString
      DOCUMENT ME!

    • datasetNameString

      private String datasetNameString
      DOCUMENT ME!

    • ddof

      private int ddof
      DOCUMENT ME!

    • delta

      private float[] delta
      DOCUMENT ME!

    • dicomDelta

      private float[] dicomDelta
      DOCUMENT ME!

    • dicomHighestX

      private float dicomHighestX
      DOCUMENT ME!

    • dicomHighestY

      private float dicomHighestY
      DOCUMENT ME!

    • dicomHighestZ

      private float dicomHighestZ
      DOCUMENT ME!

    • dicomLowestX

      private float dicomLowestX
      Dicom ordered bounding box in mm.

    • dicomLowestY

      private float dicomLowestY
      Dicom ordered bounding box in mm.

    • dicomLowestZ

      private float dicomLowestZ
      Dicom ordered bounding box in mm.

    • dicomOrientation

      private int[] dicomOrientation
      DOCUMENT ME!

    • dicomOrigin

      private float[] dicomOrigin
      DOCUMENT ME!

    • dicomSliceSize

      private int dicomSliceSize
      DOCUMENT ME!

    • dicomXDim

      private int dicomXDim
      DOCUMENT ME!

    • dicomYDim

      private int dicomYDim
      DOCUMENT ME!

    • dicomZDim

      private int dicomZDim
      DOCUMENT ME!

    • dist_ant

      private float dist_ant
      DOCUMENT ME!

    • dist_med

      private float dist_med
      DOCUMENT ME!

    • dist_pos

      private float dist_pos
      DOCUMENT ME!

    • dist_sup

      private float dist_sup
      DOCUMENT ME!

    • dist_inf

      private float dist_inf
      DOCUMENT ME!

    • dist_lef

      private float dist_lef
      DOCUMENT ME!

    • dist_rig

      private float dist_rig
      DOCUMENT ME!

    • doDicom

      private boolean doDicom
      DOCUMENT ME!

    • dof

      private int dof
      FUNC_TT_TYPE Student t Degrees-of-Freedom (DOF).

    • endianess

      private boolean endianess
      DOCUMENT ME!

    • file

      private File file
      DOCUMENT ME!

    • fileDir

      private String fileDir
      DOCUMENT ME!

    • fileInfo

      private FileInfoAfni fileInfo
      DOCUMENT ME!

    • fileInfoCopy

      private FileInfoAfni fileInfoCopy

    • fileLength

      private long fileLength
      DOCUMENT ME!

    • fileName

      private String fileName
      DOCUMENT ME!

    • firstPtDicom

      private WildMagic.LibFoundation.Mathematics.Vector3f firstPtDicom
      DOCUMENT ME!

    • floatsPerTag

      private int floatsPerTag
      DOCUMENT ME!

    • funcType

      private int funcType
      DOCUMENT ME!

    • haveReadACPC

      private boolean haveReadACPC
      DOCUMENT ME!

    • haveReadOrig

      private boolean haveReadOrig
      DOCUMENT ME!

    • historyNoteString

      private String historyNoteString
      DOCUMENT ME!

    • idcodeAnatParentString

      private String idcodeAnatParentString
      DOCUMENT ME!

    • idcodeDateString

      private String idcodeDateString
      DOCUMENT ME!

    • idcodeString

      private String idcodeString
      DOCUMENT ME!

    • idcodeWarpParentString

      private String idcodeWarpParentString
      DOCUMENT ME!

    • image

      private ModelImage image
      DOCUMENT ME!

    • img2Buffer

      private float[] img2Buffer
      DOCUMENT ME!

    • imgBuffer

      private float[] imgBuffer
      DOCUMENT ME!

    • imgExtents

      private int[] imgExtents
      DOCUMENT ME!

    • imgResols

      private float[] imgResols
      DOCUMENT ME!

    • invertX

      private boolean invertX
      DOCUMENT ME!

    • invertY

      private boolean invertY
      DOCUMENT ME!

    • invertZ

      private boolean invertZ
      DOCUMENT ME!

    • label1String

      private String label1String
      DOCUMENT ME!

    • label2String

      private String label2String
      DOCUMENT ME!

    • loadB

      private boolean loadB
      DOCUMENT ME!

    • lowestX

      private float lowestX
      Dataset ordered bounding box in mm.

    • lowestY

      private float lowestY
      Dataset ordered bounding box in mm.

    • lowestZ

      private float lowestZ
      Dataset ordered bounding box in mm.

    • highestX

      private float highestX
      Dataset ordered bounding box in mm.

    • highestY

      private float highestY
      Dataset ordered bounding box in mm.

    • highestZ

      private float highestZ
      Dataset ordered bounding box in mm.

    • marksFlag

      private int marksFlag
      DOCUMENT ME!

    • marksFlags

      private int marksFlags
      DOCUMENT ME!

    • marksHelpString

      private String[] marksHelpString
      DOCUMENT ME!

    • marksLabString

      private String[] marksLabString
      DOCUMENT ME!

    • marksXYZ

      private float[] marksXYZ
      DOCUMENT ME!

    • ndof

      private int ndof
      FUNC_FT_TYPE F ratio Numerator DOF, Denominator DOF.

    • noteDate001String

      private String noteDate001String
      DOCUMENT ME!

    • noteDate002String

      private String noteDate002String
      DOCUMENT ME!

    • noteDate003String

      private String noteDate003String
      DOCUMENT ME!

    • noteDate004String

      private String noteDate004String
      DOCUMENT ME!

    • noteDate005String

      private String noteDate005String
      DOCUMENT ME!

    • noteNumber001String

      private String noteNumber001String
      DOCUMENT ME!

    • noteNumber002String

      private String noteNumber002String
      DOCUMENT ME!

    • noteNumber003String

      private String noteNumber003String
      DOCUMENT ME!

    • noteNumber004String

      private String noteNumber004String
      DOCUMENT ME!

    • noteNumber005String

      private String noteNumber005String
      DOCUMENT ME!

    • notesCount

      private int notesCount
      DOCUMENT ME!

    • numberDicomSlices

      private int numberDicomSlices
      DOCUMENT ME!

    • numberSlices

      private int numberSlices
      DOCUMENT ME!

    • numFitParam

      private int numFitParam
      DOCUMENT ME!

    • numNuisanceParam

      private int numNuisanceParam
      DOCUMENT ME!

    • numSamples

      private int numSamples
      DOCUMENT ME!

    • numTrials

      private int numTrials
      FUNC_BN_TYPE Binomial # Trials, Probability per trial.

    • orientSpecific

      private int[] orientSpecific
      DOCUMENT ME!

    • origAC

      private WildMagic.LibFoundation.Mathematics.Vector3f origAC
      DOCUMENT ME!

    • origDelta

      private float[] origDelta
      DOCUMENT ME!

    • origDicom

      private boolean origDicom
      DOCUMENT ME!

    • origExtents

      private int[] origExtents
      DOCUMENT ME!

    • origin

      private float[] origin
      DOCUMENT ME!

    • originalFileName

      private String originalFileName
      DOCUMENT ME!

    • origName

      private String origName
      DOCUMENT ME!

    • origOrigin

      private float[] origOrigin
      DOCUMENT ME!

    • origXDim

      private int origXDim
      DOCUMENT ME!

    • origYDim

      private int origYDim
      DOCUMENT ME!

    • origZDim

      private int origZDim
      DOCUMENT ME!

    • pcDicom

      private WildMagic.LibFoundation.Mathematics.Vector3f pcDicom
      DOCUMENT ME!

    • pointMarker

      private WildMagic.LibFoundation.Mathematics.Vector3f pointMarker
      DOCUMENT ME!

    • posteriorMarginDicom

      private WildMagic.LibFoundation.Mathematics.Vector3f posteriorMarginDicom
      DOCUMENT ME!

    • presentViewType

      private int presentViewType
      DOCUMENT ME!

    • readACPC

      private boolean readACPC
      DOCUMENT ME!

    • readTLRC

      private boolean readTLRC
      DOCUMENT ME!

    • scale_A

      private float scale_A
      DOCUMENT ME!

    • scale_M

      private float scale_M
      DOCUMENT ME!

    • scale_P

      private float scale_P
      DOCUMENT ME!

    • scale_S

      private float scale_S
      DOCUMENT ME!

    • scale_I

      private float scale_I
      DOCUMENT ME!

    • scale_L

      private float scale_L
      DOCUMENT ME!

    • scale_R

      private float scale_R
      DOCUMENT ME!

    • skip

      private float[] skip
      DOCUMENT ME!

    • sliceSize

      private int sliceSize
      DOCUMENT ME!

    • slicesWithTimeOffsets

      private int slicesWithTimeOffsets
      DOCUMENT ME!

    • statAux

      private float[] statAux
      # orts are nuisance parameters whose number is >= 1.

    • statCode

      private int statCode
      DOCUMENT ME!

    • subBrickIndex

      private int subBrickIndex
      DOCUMENT ME!

    • subBrickNumber

      private int subBrickNumber
      DOCUMENT ME!

    • superiorEdgeDicom

      private WildMagic.LibFoundation.Mathematics.Vector3f superiorEdgeDicom
      DOCUMENT ME!

    • tagAlignMatvec

      private float[] tagAlignMatvec
      The "p-values" for fico, fitt, and fizt datasets are 2-sided: that is, the value displayed by AFNI (below the slider) is the probability that the absolute value of such a deviate will exceed the threshold value on the slider. The "p-values" for the other types are 1-sided: that is, the value displayed by AFNI is the probability that the value of the deviate will exceed the threshold value. (Of course, these probabilities are computed under the appropriate null hypothesis, and assuming that the distributional model holds exactly. The latter assumption, in particular, is fairly dubious.) Registration attributes Note that the MATVEC attributes are transformations of Dicom-ordered coordinates, and so have to be permuted to transform dataset-ordered xyz-coordinates. The MATVEC attributes describe the transformation of coordinates from the input dataset to the output dataset in the form [xyz_out] = [mat] ([xyz_in] - [xyz_cen]) + [vec] + [xyz_cen] where [mat] is a 3x3 orthogonal matrix [vec] is a 3-vector [xyz_in] is the input vector [xyz_cen] is the center of rotation (usually the center of the dataset) [xyz_out] is the output vector Dicom coordinate order is used for these matrices and vectors, which means that they need to be permuted to dataset order for application

    • tagNumber

      private int tagNumber
      DOCUMENT ME!

    • tagsetFloats

      private float[] tagsetFloats
      DOCUMENT ME!

    • tagsetLabelsString

      private String tagsetLabelsString
      2560 characters giving the help strings for the markers (256 chars per marker, EXACTLY, including the NULS).

    • tAxisOffsets

      private float[] tAxisOffsets
      DOCUMENT ME!

    • tDim

      private int tDim
      DOCUMENT ME!

    • timeOrigin

      private float timeOrigin
      DOCUMENT ME!

    • timeStep

      private float timeStep
      DOCUMENT ME!

    • timeStepUnit

      private int timeStepUnit
      DOCUMENT ME!

    • tInfo

      private TalairachTransformInfo tInfo
      DOCUMENT ME!

    • tlrcRes

      private float[] tlrcRes
      DOCUMENT ME!

    • typeString

      private String typeString
      DOCUMENT ME!

    • typeStringType

      private int typeStringType
      DOCUMENT ME!

    • UI

      private ViewUserInterface UI
      DOCUMENT ME!

    • viewType

      private int viewType
      DOCUMENT ME!

    • volregBaseIdcodeString

      private String volregBaseIdcodeString
      DOCUMENT ME!

    • volregBaseNameString

      private String volregBaseNameString
      DOCUMENT ME!

    • volregCenterBase

      private float[] volregCenterBase
      DOCUMENT ME!

    • volregCenterOld

      private float[] volregCenterOld
      For sub-brick #xxxxxx (so a max of 999,999 sub-bricks can be used), this stores 12 numbers for the matrix-vector of transformation from 3dvolreg.

    • volregGridparentIdcodeString

      private String volregGridparentIdcodeString
      DOCUMENT ME!

    • volregGridparentNameString

      private String volregGridparentNameString
      DOCUMENT ME!

    • volregInputIdcodeString

      private String volregInputIdcodeString
      DOCUMENT ME!

    • volregInputNameString

      private String volregInputNameString
      DOCUMENT ME!

    • volregMatvec000000

      private float[] volregMatvec000000
      DOCUMENT ME!

    • volregMatvec000001

      private float[] volregMatvec000001
      DOCUMENT ME!

    • volregMatvec000002

      private float[] volregMatvec000002
      DOCUMENT ME!

    • volregMatvec000003

      private float[] volregMatvec000003
      DOCUMENT ME!

    • volregMatvec000004

      private float[] volregMatvec000004
      DOCUMENT ME!

    • volregMatvec000005

      private float[] volregMatvec000005
      DOCUMENT ME!

    • volregMatvec000006

      private float[] volregMatvec000006
      DOCUMENT ME!

    • volregMatvec000007

      private float[] volregMatvec000007
      DOCUMENT ME!

    • volregMatvec000008

      private float[] volregMatvec000008
      DOCUMENT ME!

    • volregMatvec000009

      private float[] volregMatvec000009
      DOCUMENT ME!

    • volregRotcomNum

      private int volregRotcomNum
      DOCUMENT ME!

    • volregRotparentIdcodeString

      private String volregRotparentIdcodeString
      DOCUMENT ME!

    • volregRotparentNameString

      private String volregRotparentNameString
      DOCUMENT ME!

    • warpData

      private float[] warpData
      DOCUMENT ME!

    • warpParentnameString

      private String warpParentnameString
      DOCUMENT ME!

    • warpType

      private int warpType
      DOCUMENT ME!

    • xDim

      private int xDim
      DOCUMENT ME!

    • yDim

      private int yDim
      DOCUMENT ME!

    • zAxisOffset

      private float zAxisOffset
      DOCUMENT ME!

    • zAxisStep

      private float zAxisStep
      DOCUMENT ME!

    • zDim

      private int zDim
      DOCUMENT ME!

    • zeroPad

      private int[] zeroPad
      DOCUMENT ME!

  • Constructor Details

    • FileAfni

      public FileAfni(String fileName, String fileDir, boolean loadB, boolean doRead) throws IOException
      Afni reader constructor.
      Parameters:
      fileName - file name
      fileDir - file directory
      loadB - flag indicating if this is a B image
      doRead - whether class is created for reading afni file, or for writing
      Throws:
      IOException - if there is an error making the file

  • 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 FileInfoBase getFileInfo()
      getFileInfo - accessor that returns the file info.
      Returns:
      FileInfoBase containing the file info

    • getImageBuffer

      public float[] getImageBuffer()
      getImageBuffer - accessor that returns the image buffer.
      Returns:
      buffer of image.

    • readImage

      public ModelImage readImage() throws IOException
      readImage.
      Returns:
      returns the image
      Throws:
      IOException - if there is an error reading the file

    • setFileName

      public void setFileName(String fName)
      setFileName - accessor to set the file name (used when reading TIFF multiFile).
      Parameters:
      fName - file name of image to read.

    • getModelLUT

      public ModelLUT getModelLUT()

    • writeImage

      public void writeImage(ModelImage image, FileWriteOptions options) throws IOException
      Writes a AFNI 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

    • calcOriginalMarker

      private void calcOriginalMarker(int markerNumber)
      DOCUMENT ME!
      Parameters:
      markerNumber - DOCUMENT ME!

    • createOrderDialog

      private void createOrderDialog()
      DOCUMENT ME!

    • crossProduct

      private WildMagic.LibFoundation.Mathematics.Vector3f crossProduct(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)
      Finds crossproduct of two vectors.
      Parameters:
      pt1 - First vector.
      pt2 - Second vector
      Returns:
      Cross product of pt1 and pt2.

    • dicomMarker

      private WildMagic.LibFoundation.Mathematics.Vector3f dicomMarker(WildMagic.LibFoundation.Mathematics.Vector3f pMarker)
      DOCUMENT ME!
      Parameters:
      pMarker - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • dist

      private float dist(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2, float[] resol)
      DOCUMENT ME!
      Parameters:
      pt1 - DOCUMENT ME!
      pt2 - DOCUMENT ME!
      resol - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • dotProduct

      private float dotProduct(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)
      DOCUMENT ME!
      Parameters:
      pt1 - DOCUMENT ME!
      pt2 - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • makemmVector3f

      private WildMagic.LibFoundation.Mathematics.Vector3f makemmVector3f(WildMagic.LibFoundation.Mathematics.Vector3f pt, float[] resol)
      DOCUMENT ME!
      Parameters:
      pt - DOCUMENT ME!
      resol - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • makeVoxelCoord3Df

      private WildMagic.LibFoundation.Mathematics.Vector3f makeVoxelCoord3Df(WildMagic.LibFoundation.Mathematics.Vector3f pt, float[] resol)
      DOCUMENT ME!
      Parameters:
      pt - DOCUMENT ME!
      resol - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • norm

      private WildMagic.LibFoundation.Mathematics.Vector3f norm(WildMagic.LibFoundation.Mathematics.Vector3f pt)
      Finds the normal to the vector.
      Parameters:
      pt - Vector to find normal to.
      Returns:
      Normal of pt.

    • readBuffer

      public void readBuffer(int slice, float[] buffer, float scaleFact, int numRead) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is stored
      scaleFact - if zero data unscaled, if > 0 data is scaled by scaleFact
      numRead - DOCUMENT ME!
      Throws:
      IOException - if there is an error reading the file

    • readHeader

      public boolean readHeader() throws IOException
      Reads AFNI header (.HEAD file)
      Throws:
      IOException - if there is an error reading the file

    • readImage2

      private ModelImage readImage2() throws IOException
      Reads AFNI image (.BRIK file)
      Returns:
      Generated modelImage
      Throws:
      IOException - data reading problem occured

    • readLine

      private String readLine() throws IOException
      readLine() - reads a line of the file and strips comments indicated by the # symbol.
      Returns:
      the line read in
      Throws:
      IOException - if there is an error reading the file

    • readXYZBuffer

      public void readXYZBuffer(int slice, float[] buffer, float[] dicomBuffer, float scaleFact) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is read into
      dicomBuffer - buffer into which the data is reordered
      scaleFact - if zero data unscaled, if > 0 data is scaled by scaleFact
      Throws:
      IOException - if there is an error reading the file

    • removeWhiteSpace

      private String removeWhiteSpace(String inString)
      DOCUMENT ME!
      Parameters:
      inString - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • reposMarker

      private void reposMarker(int markerNumber)
      DOCUMENT ME!
      Parameters:
      markerNumber - DOCUMENT ME!

    • sclAdd

      private WildMagic.LibFoundation.Mathematics.Vector3f sclAdd(float fa, WildMagic.LibFoundation.Mathematics.Vector3f a, float fb, WildMagic.LibFoundation.Mathematics.Vector3f b)
      scale and add two vectors.
      Parameters:
      fa - DOCUMENT ME!
      a - DOCUMENT ME!
      fb - DOCUMENT ME!
      b - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • sub

      private WildMagic.LibFoundation.Mathematics.Vector3f sub(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)
      DOCUMENT ME!
      Parameters:
      pt1 - DOCUMENT ME!
      pt2 - DOCUMENT ME!
      Returns:
      DOCUMENT ME!

    • transformACPCTrilinear

      private void transformACPCTrilinear(float[] imgBuffer, TransMatrix xfrm, float iXres, float iYres, float iZres, int iXdim, int iYdim, int iZdim, float oXres, float oYres, float oZres, int oXdim, int oYdim, int oZdim)
      transformACPCTrilinear - transforms and resamples volume using trilinear interpolation.
      Parameters:
      imgBuffer - image array
      xfrm - transformation matrix to be applied
      iXres - DOCUMENT ME!
      iYres - DOCUMENT ME!
      iZres - DOCUMENT ME!
      iXdim - DOCUMENT ME!
      iYdim - DOCUMENT ME!
      iZdim - DOCUMENT ME!
      oXres - DOCUMENT ME!
      oYres - DOCUMENT ME!
      oZres - DOCUMENT ME!
      oXdim - DOCUMENT ME!
      oYdim - DOCUMENT ME!
      oZdim - DOCUMENT ME!

    • transformTalairachTrilinear

      private void transformTalairachTrilinear(float[] imgBuffer, TransMatrix xfrm, float iXres, float iYres, float iZres, int iXdim, int iYdim, int iZdim, float oXres, float oYres, float oZres, int oXdim, int botX, int botY, int botZ, int topX, int topY, int topZ)
      transformTalairachTrilinear - transforms and resamples volume using trilinear interpolation.
      Parameters:
      imgBuffer - image array
      xfrm - transformation matrix to be applied
      iXres - DOCUMENT ME!
      iYres - DOCUMENT ME!
      iZres - DOCUMENT ME!
      iXdim - DOCUMENT ME!
      iYdim - DOCUMENT ME!
      iZdim - DOCUMENT ME!
      oXres - DOCUMENT ME!
      oYres - DOCUMENT ME!
      oZres - DOCUMENT ME!
      oXdim - DOCUMENT ME!
      botX - DOCUMENT ME!
      botY - DOCUMENT ME!
      botZ - DOCUMENT ME!
      topX - DOCUMENT ME!
      topY - DOCUMENT ME!
      topZ - DOCUMENT ME!