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:

FileIO

Field Summary

Fields
Modifier and Type	Field	Description
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`acpcAC`	Anterior Comissure in acpc space.
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`acpcMaxPt`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`acpcMinPt`	DOCUMENT ME!
`private java.lang.String`	`acpcName`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`acpcPC`	DOCUMENT ME!
`private float`	`acpcRes`	DOCUMENT ME!
`private float`	`acquisitionDuration`	DOCUMENT ME!
`private boolean`	`alsoAcpc`	DOCUMENT ME!
`private boolean`	`alsoOrig`	DOCUMENT ME!
`static int`	`ANAT_BMAP_TYPE`	DOCUMENT ME!
`static int`	`ANAT_BUCK_TYPE`	DOCUMENT ME!
`static int`	`ANAT_CT_TYPE`	DOCUMENT ME!
`static int`	`ANAT_DIFF_TYPE`	DOCUMENT ME!
`static int`	`ANAT_EPI_TYPE`	DOCUMENT ME!
`static int`	`ANAT_FSE_TYPE`	DOCUMENT ME!
`static int`	`ANAT_MRA_TYPE`	DOCUMENT ME!
`static int`	`ANAT_MRAN_TYPE`	DOCUMENT ME!
`static int`	`ANAT_OMRI_TYPE`	DOCUMENT ME!
`static int`	`ANAT_PET_TYPE`	DOCUMENT ME!
`static int`	`ANAT_SPECT_TYPE`	DOCUMENT ME!
`static int`	`ANAT_SPGR_TYPE`	funcType for anatType == true.
`private java.lang.String`	`anatomyParentnameString`	DOCUMENT ME!
`private boolean`	`anatType`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`anotherPtDicom`	DOCUMENT ME!
`private static float`	`ATLAS_AC_TO_LAT`	DOCUMENT ME!
`private static float`	`ATLAS_AC_TO_TOP`	DOCUMENT ME!
`private static float`	`ATLAS_BOT_TO_AC`	DOCUMENT ME!
`private static float`	`ATLAS_FRONT_TO_AC`	DOCUMENT ME!
`private static float`	`ATLAS_PC_TO_BACK`	DOCUMENT ME!
`private float[]`	`brickFloatFacs`	DOCUMENT ME!
`private java.lang.String`	`brickKeywordsString`	DOCUMENT ME!
`private java.lang.String[]`	`brickLabsString`	Sub-brick names
`private float[]`	`brickStatAux`	Each BLT is defined by a struct that contains two 3x3 matrices and four 3-vectors (233 + 4*3 = the 30 numbers).
`private float[]`	`brickStats`	DOCUMENT ME!
`private int`	`brickType`	DOCUMENT ME!
`private int`	`brickTypeNumber`	DOCUMENT ME!
`private int`	`brikDataType`	DOCUMENT ME!
`private java.lang.String`	`brikFileName`	DOCUMENT ME!
`private int`	`bufferSize`	DOCUMENT ME!
`private int[]`	`dataExtents`	DOCUMENT ME!
`private int[]`	`dataOrient`	DOCUMENT ME!
`private java.lang.String`	`datasetKeywordsString`	DOCUMENT ME!
`private java.lang.String`	`datasetNameString`	DOCUMENT ME!
`private int`	`ddof`	DOCUMENT ME!
`private float[]`	`delta`	DOCUMENT ME!
`private float[]`	`dicomDelta`	DOCUMENT ME!
`private float`	`dicomHighestX`	DOCUMENT ME!
`private float`	`dicomHighestY`	DOCUMENT ME!
`private float`	`dicomHighestZ`	DOCUMENT ME!
`private float`	`dicomLowestX`	Dicom ordered bounding box in mm.
`private float`	`dicomLowestY`	Dicom ordered bounding box in mm.
`private float`	`dicomLowestZ`	Dicom ordered bounding box in mm.
`private int[]`	`dicomOrientation`	DOCUMENT ME!
`private float[]`	`dicomOrigin`	DOCUMENT ME!
`private int`	`dicomSliceSize`	DOCUMENT ME!
`private int`	`dicomXDim`	DOCUMENT ME!
`private int`	`dicomYDim`	DOCUMENT ME!
`private int`	`dicomZDim`	DOCUMENT ME!
`private float`	`dist_ant`	DOCUMENT ME!
`private float`	`dist_inf`	DOCUMENT ME!
`private float`	`dist_lef`	DOCUMENT ME!
`private float`	`dist_med`	DOCUMENT ME!
`private float`	`dist_pos`	DOCUMENT ME!
`private float`	`dist_rig`	DOCUMENT ME!
`private float`	`dist_sup`	DOCUMENT ME!
`private boolean`	`doDicom`	DOCUMENT ME!
`private int`	`dof`	FUNC_TT_TYPE Student t Degrees-of-Freedom (DOF).
`private boolean`	`endianess`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoAfni`	`fileInfo`	DOCUMENT ME!
`private FileInfoAfni`	`fileInfoCopy`
`private long`	`fileLength`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`firstPtDicom`	DOCUMENT ME!
`static int`	`FLOAT_ATTRIBUTE`	DOCUMENT ME!
`private int`	`floatsPerTag`	DOCUMENT ME!
`static float`	`FUNC_BN_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_BN_TYPE`	DOCUMENT ME!
`static float`	`FUNC_BT_SCALE_BYTE`	DOCUMENT ME!
`static float`	`FUNC_BT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_BT_TYPE`	DOCUMENT ME!
`static int`	`FUNC_BUCK_TYPE`	DOCUMENT ME!
`static float`	`FUNC_COR_SCALE_BYTE`	DOCUMENT ME!
`static float`	`FUNC_COR_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_COR_TYPE`	DOCUMENT ME!
`static float`	`FUNC_CT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_CT_TYPE`	DOCUMENT ME!
`static int`	`FUNC_FIM_TYPE`	funcType for anatType == false.
`static float`	`FUNC_FT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_FT_TYPE`	DOCUMENT ME!
`static float`	`FUNC_GT_SCALE_BYTE`	DOCUMENT ME!
`static float`	`FUNC_GT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_GT_TYPE`	DOCUMENT ME!
`static float`	`FUNC_PT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_PT_TYPE`	DOCUMENT ME!
`static float`	`FUNC_THR_SCALE_BYTE`	6 funcType of functional data have default scaling for byte data.
`static float`	`FUNC_THR_SCALE_SHORT`	Unfortunately, the func type codes overlap for Func and Anat datasets.
`static int`	`FUNC_THR_TYPE`	DOCUMENT ME!
`static float`	`FUNC_TT_SCALE_BYTE`	DOCUMENT ME!
`static float`	`FUNC_TT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_TT_TYPE`	DOCUMENT ME!
`static float`	`FUNC_ZT_SCALE_BYTE`	DOCUMENT ME!
`static float`	`FUNC_ZT_SCALE_SHORT`	DOCUMENT ME!
`static int`	`FUNC_ZT_TYPE`	DOCUMENT ME!
`private int`	`funcType`	DOCUMENT ME!
`private boolean`	`haveReadACPC`	DOCUMENT ME!
`private boolean`	`haveReadOrig`	DOCUMENT ME!
`private float`	`highestX`	Dataset ordered bounding box in mm.
`private float`	`highestY`	Dataset ordered bounding box in mm.
`private float`	`highestZ`	Dataset ordered bounding box in mm.
`private java.lang.String`	`historyNoteString`	DOCUMENT ME!
`private java.lang.String`	`idcodeAnatParentString`	DOCUMENT ME!
`private java.lang.String`	`idcodeDateString`	DOCUMENT ME!
`private java.lang.String`	`idcodeString`	DOCUMENT ME!
`private java.lang.String`	`idcodeWarpParentString`	DOCUMENT ME!
`private ModelImage`	`image`	DOCUMENT ME!
`private float[]`	`img2Buffer`	DOCUMENT ME!
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private int[]`	`imgExtents`	DOCUMENT ME!
`private float[]`	`imgResols`	DOCUMENT ME!
`static int`	`INTEGER_ATTRIBUTE`	attribute types.
`private boolean`	`invertX`	DOCUMENT ME!
`private boolean`	`invertY`	DOCUMENT ME!
`private boolean`	`invertZ`	DOCUMENT ME!
`private java.lang.String`	`label1String`	DOCUMENT ME!
`private java.lang.String`	`label2String`	DOCUMENT ME!
`private boolean`	`loadB`	DOCUMENT ME!
`private float`	`lowestX`	Dataset ordered bounding box in mm.
`private float`	`lowestY`	Dataset ordered bounding box in mm.
`private float`	`lowestZ`	Dataset ordered bounding box in mm.
`static int`	`MARKSET_ALIGN`	marker types.
`static int`	`MARKSET_BOUNDING`	DOCUMENT ME!
`private int`	`marksFlag`	DOCUMENT ME!
`private int`	`marksFlags`	DOCUMENT ME!
`private java.lang.String[]`	`marksHelpString`	DOCUMENT ME!
`private java.lang.String[]`	`marksLabString`	DOCUMENT ME!
`private float[]`	`marksXYZ`	DOCUMENT ME!
`private int`	`ndof`	FUNC_FT_TYPE F ratio Numerator DOF, Denominator DOF.
`private java.lang.String`	`noteDate001String`	DOCUMENT ME!
`private java.lang.String`	`noteDate002String`	DOCUMENT ME!
`private java.lang.String`	`noteDate003String`	DOCUMENT ME!
`private java.lang.String`	`noteDate004String`	DOCUMENT ME!
`private java.lang.String`	`noteDate005String`	DOCUMENT ME!
`private java.lang.String`	`noteNumber001String`	DOCUMENT ME!
`private java.lang.String`	`noteNumber002String`	DOCUMENT ME!
`private java.lang.String`	`noteNumber003String`	DOCUMENT ME!
`private java.lang.String`	`noteNumber004String`	DOCUMENT ME!
`private java.lang.String`	`noteNumber005String`	DOCUMENT ME!
`private int`	`notesCount`	DOCUMENT ME!
`private int`	`numberDicomSlices`	DOCUMENT ME!
`private int`	`numberSlices`	DOCUMENT ME!
`private int`	`numFitParam`	DOCUMENT ME!
`private int`	`numNuisanceParam`	DOCUMENT ME!
`private int`	`numSamples`	DOCUMENT ME!
`private int`	`numTrials`	FUNC_BN_TYPE Binomial # Trials, Probability per trial.
`private int[]`	`orientSpecific`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`origAC`	DOCUMENT ME!
`private float[]`	`origDelta`	DOCUMENT ME!
`private boolean`	`origDicom`	DOCUMENT ME!
`private int[]`	`origExtents`	DOCUMENT ME!
`private float[]`	`origin`	DOCUMENT ME!
`private java.lang.String`	`originalFileName`	DOCUMENT ME!
`private java.lang.String`	`origName`	DOCUMENT ME!
`private float[]`	`origOrigin`	DOCUMENT ME!
`private int`	`origXDim`	DOCUMENT ME!
`private int`	`origYDim`	DOCUMENT ME!
`private int`	`origZDim`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`pcDicom`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`pointMarker`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`posteriorMarginDicom`	DOCUMENT ME!
`private int`	`presentViewType`	DOCUMENT ME!
`private boolean`	`readACPC`	DOCUMENT ME!
`private boolean`	`readTLRC`	DOCUMENT ME!
`private float`	`scale_A`	DOCUMENT ME!
`private float`	`scale_I`	DOCUMENT ME!
`private float`	`scale_L`	DOCUMENT ME!
`private float`	`scale_M`	DOCUMENT ME!
`private float`	`scale_P`	DOCUMENT ME!
`private float`	`scale_R`	DOCUMENT ME!
`private float`	`scale_S`	DOCUMENT ME!
`private float[]`	`skip`	DOCUMENT ME!
`private int`	`sliceSize`	DOCUMENT ME!
`private int`	`slicesWithTimeOffsets`	DOCUMENT ME!
`private float[]`	`statAux`	# orts are nuisance parameters whose number is >= 1.
`private int`	`statCode`	DOCUMENT ME!
`static int`	`STRING_ATTRIBUTE`	DOCUMENT ME!
`private int`	`subBrickIndex`	DOCUMENT ME!
`private int`	`subBrickNumber`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`superiorEdgeDicom`	DOCUMENT ME!
`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.
`private int`	`tagNumber`	DOCUMENT ME!
`private float[]`	`tagsetFloats`	DOCUMENT ME!
`private java.lang.String`	`tagsetLabelsString`	2560 characters giving the help strings for the markers (256 chars per marker, EXACTLY, including the NULS).
`private float[]`	`tAxisOffsets`	DOCUMENT ME!
`private int`	`tDim`	DOCUMENT ME!
`private float`	`timeOrigin`	DOCUMENT ME!
`private float`	`timeStep`	DOCUMENT ME!
`private int`	`timeStepUnit`	DOCUMENT ME!
`private TalairachTransformInfo`	`tInfo`	DOCUMENT ME!
`private float[]`	`tlrcRes`	DOCUMENT ME!
`private java.lang.String`	`typeString`	DOCUMENT ME!
`private int`	`typeStringType`	DOCUMENT ME!
`private ViewUserInterface`	`UI`	DOCUMENT ME!
`static int`	`UNITS_HZ_TYPE`	DOCUMENT ME!
`static int`	`UNITS_MSEC_TYPE`	time step units.
`static int`	`UNITS_SEC_TYPE`	DOCUMENT ME!
`private int`	`viewType`	DOCUMENT ME!
`private java.lang.String`	`volregBaseIdcodeString`	DOCUMENT ME!
`private java.lang.String`	`volregBaseNameString`	DOCUMENT ME!
`private float[]`	`volregCenterBase`	DOCUMENT ME!
`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.
`private java.lang.String`	`volregGridparentIdcodeString`	DOCUMENT ME!
`private java.lang.String`	`volregGridparentNameString`	DOCUMENT ME!
`private java.lang.String`	`volregInputIdcodeString`	DOCUMENT ME!
`private java.lang.String`	`volregInputNameString`	DOCUMENT ME!
`private float[]`	`volregMatvec000000`	DOCUMENT ME!
`private float[]`	`volregMatvec000001`	DOCUMENT ME!
`private float[]`	`volregMatvec000002`	DOCUMENT ME!
`private float[]`	`volregMatvec000003`	DOCUMENT ME!
`private float[]`	`volregMatvec000004`	DOCUMENT ME!
`private float[]`	`volregMatvec000005`	DOCUMENT ME!
`private float[]`	`volregMatvec000006`	DOCUMENT ME!
`private float[]`	`volregMatvec000007`	DOCUMENT ME!
`private float[]`	`volregMatvec000008`	DOCUMENT ME!
`private float[]`	`volregMatvec000009`	DOCUMENT ME!
`private int`	`volregRotcomNum`	DOCUMENT ME!
`private java.lang.String`	`volregRotparentIdcodeString`	DOCUMENT ME!
`private java.lang.String`	`volregRotparentNameString`	DOCUMENT ME!
`static int`	`WARP_AFFINE_TYPE`	warp types.
`static int`	`WARP_TALAIRACH_12_TYPE`	DOCUMENT ME!
`private float[]`	`warpData`	DOCUMENT ME!
`private java.lang.String`	`warpParentnameString`	DOCUMENT ME!
`private int`	`warpType`	DOCUMENT ME!
`private int`	`xDim`	DOCUMENT ME!
`private int`	`yDim`	DOCUMENT ME!
`private float`	`zAxisOffset`	DOCUMENT ME!
`private float`	`zAxisStep`	DOCUMENT ME!
`private int`	`zDim`	DOCUMENT ME!
`private int[]`	`zeroPad`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.file.FileBase
BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors
Constructor Description

FileAfni(java.lang.String fileName, java.lang.String fileDir, boolean loadB, boolean doRead)
Afni reader constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcOriginalMarker(int markerNumber)`	DOCUMENT ME!
`private void`	`createOrderDialog()`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`crossProduct(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)`	Finds crossproduct of two vectors.
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`dicomMarker(WildMagic.LibFoundation.Mathematics.Vector3f pMarker)`	DOCUMENT ME!
`private float`	`dist(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2, float[] resol)`	DOCUMENT ME!
`private float`	`dotProduct(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)`	DOCUMENT ME!
`void`	`finalize()`	Prepares this class for cleanup.
`FileInfoBase`	`getFileInfo()`	getFileInfo - accessor that returns the file info.
`float[]`	`getImageBuffer()`	getImageBuffer - accessor that returns the image buffer.
`ModelLUT`	`getModelLUT()`
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`makemmVector3f(WildMagic.LibFoundation.Mathematics.Vector3f pt, float[] resol)`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`makeVoxelCoord3Df(WildMagic.LibFoundation.Mathematics.Vector3f pt, float[] resol)`	DOCUMENT ME!
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`norm(WildMagic.LibFoundation.Mathematics.Vector3f pt)`	Finds the normal to the vector.
`void`	`readBuffer(int slice, float[] buffer, float scaleFact, int numRead)`	Reads a slice of data at a time and stores the results in the buffer.
`boolean`	`readHeader()`	Reads AFNI header (.HEAD file)
`ModelImage`	`readImage()`	readImage.
`private ModelImage`	`readImage2()`	Reads AFNI image (.BRIK file)
`private java.lang.String`	`readLine()`	readLine() - reads a line of the file and strips comments indicated by the # symbol.
`void`	`readXYZBuffer(int slice, float[] buffer, float[] dicomBuffer, float scaleFact)`	Reads a slice of data at a time and stores the results in the buffer.
`private java.lang.String`	`removeWhiteSpace(java.lang.String inString)`	DOCUMENT ME!
`private void`	`reposMarker(int markerNumber)`	DOCUMENT ME!
`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.
`void`	`setFileName(java.lang.String fName)`	setFileName - accessor to set the file name (used when reading TIFF multiFile).
`private WildMagic.LibFoundation.Mathematics.Vector3f`	`sub(WildMagic.LibFoundation.Mathematics.Vector3f pt1, WildMagic.LibFoundation.Mathematics.Vector3f pt2)`	DOCUMENT ME!
`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.
`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.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes a AFNI format type image.

Methods inherited from class gov.nih.mipav.model.file.FileBase
addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - INTEGER_ATTRIBUTE
```
public static final int INTEGER_ATTRIBUTE
```
    attribute types.
    
    See Also:
    
    Constant Field Values
  - FLOAT_ATTRIBUTE
```
public static final int FLOAT_ATTRIBUTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - STRING_ATTRIBUTE
```
public static final int STRING_ATTRIBUTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_SPGR_TYPE
```
public static final int ANAT_SPGR_TYPE
```
    funcType for anatType == true.
    
    See Also:
    
    Constant Field Values
  - ANAT_FSE_TYPE
```
public static final int ANAT_FSE_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_EPI_TYPE
```
public static final int ANAT_EPI_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_MRAN_TYPE
```
public static final int ANAT_MRAN_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_CT_TYPE
```
public static final int ANAT_CT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_SPECT_TYPE
```
public static final int ANAT_SPECT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_PET_TYPE
```
public static final int ANAT_PET_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_MRA_TYPE
```
public static final int ANAT_MRA_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_BMAP_TYPE
```
public static final int ANAT_BMAP_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_DIFF_TYPE
```
public static final int ANAT_DIFF_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_OMRI_TYPE
```
public static final int ANAT_OMRI_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ANAT_BUCK_TYPE
```
public static final int ANAT_BUCK_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_FIM_TYPE
```
public static final int FUNC_FIM_TYPE
```
    funcType for anatType == false.
    
    See Also:
    
    Constant Field Values
  - FUNC_THR_TYPE
```
public static final int FUNC_THR_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_COR_TYPE
```
public static final int FUNC_COR_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_TT_TYPE
```
public static final int FUNC_TT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_FT_TYPE
```
public static final int FUNC_FT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_ZT_TYPE
```
public static final int FUNC_ZT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_CT_TYPE
```
public static final int FUNC_CT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BT_TYPE
```
public static final int FUNC_BT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BN_TYPE
```
public static final int FUNC_BN_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_GT_TYPE
```
public static final int FUNC_GT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_PT_TYPE
```
public static final int FUNC_PT_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BUCK_TYPE
```
public static final int FUNC_BUCK_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - 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:
    
    Constant Field Values
  - FUNC_COR_SCALE_SHORT
```
public static final float FUNC_COR_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_TT_SCALE_SHORT
```
public static final float FUNC_TT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_FT_SCALE_SHORT
```
public static final float FUNC_FT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_ZT_SCALE_SHORT
```
public static final float FUNC_ZT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_CT_SCALE_SHORT
```
public static final float FUNC_CT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BT_SCALE_SHORT
```
public static final float FUNC_BT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BN_SCALE_SHORT
```
public static final float FUNC_BN_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_GT_SCALE_SHORT
```
public static final float FUNC_GT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_PT_SCALE_SHORT
```
public static final float FUNC_PT_SCALE_SHORT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_THR_SCALE_BYTE
```
public static final float FUNC_THR_SCALE_BYTE
```
    6 funcType of functional data have default scaling for byte data.
    
    See Also:
    
    Constant Field Values
  - FUNC_COR_SCALE_BYTE
```
public static final float FUNC_COR_SCALE_BYTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_TT_SCALE_BYTE
```
public static final float FUNC_TT_SCALE_BYTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_ZT_SCALE_BYTE
```
public static final float FUNC_ZT_SCALE_BYTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_BT_SCALE_BYTE
```
public static final float FUNC_BT_SCALE_BYTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - FUNC_GT_SCALE_BYTE
```
public static final float FUNC_GT_SCALE_BYTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MARKSET_ALIGN
```
public static final int MARKSET_ALIGN
```
    marker types.
    
    See Also:
    
    Constant Field Values
  - MARKSET_BOUNDING
```
public static final int MARKSET_BOUNDING
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - WARP_AFFINE_TYPE
```
public static final int WARP_AFFINE_TYPE
```
    warp types.
    
    See Also:
    
    Constant Field Values
  - WARP_TALAIRACH_12_TYPE
```
public static final int WARP_TALAIRACH_12_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - UNITS_MSEC_TYPE
```
public static final int UNITS_MSEC_TYPE
```
    time step units.
    
    See Also:
    
    Constant Field Values
  - UNITS_SEC_TYPE
```
public static final int UNITS_SEC_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - UNITS_HZ_TYPE
```
public static final int UNITS_HZ_TYPE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ATLAS_FRONT_TO_AC
```
private static final float ATLAS_FRONT_TO_AC
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ATLAS_PC_TO_BACK
```
private static final float ATLAS_PC_TO_BACK
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ATLAS_BOT_TO_AC
```
private static final float ATLAS_BOT_TO_AC
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ATLAS_AC_TO_TOP
```
private static final float ATLAS_AC_TO_TOP
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - ATLAS_AC_TO_LAT
```
private static final float ATLAS_AC_TO_LAT
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - 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 java.lang.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 java.lang.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 java.lang.String brickKeywordsString
```
    DOCUMENT ME!
  - brickLabsString
```
private java.lang.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 java.lang.String brikFileName
```
    DOCUMENT ME!
  - bufferSize
```
private int bufferSize
```
    DOCUMENT ME!
  - dataExtents
```
private int[] dataExtents
```
    DOCUMENT ME!
  - dataOrient
```
private int[] dataOrient
```
    DOCUMENT ME!
  - datasetKeywordsString
```
private java.lang.String datasetKeywordsString
```
    DOCUMENT ME!
  - datasetNameString
```
private java.lang.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 java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoAfni fileInfo
```
    DOCUMENT ME!
  - fileInfoCopy
```
private FileInfoAfni fileInfoCopy
```
  - fileLength
```
private long fileLength
```
    DOCUMENT ME!
  - fileName
```
private java.lang.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 java.lang.String historyNoteString
```
    DOCUMENT ME!
  - idcodeAnatParentString
```
private java.lang.String idcodeAnatParentString
```
    DOCUMENT ME!
  - idcodeDateString
```
private java.lang.String idcodeDateString
```
    DOCUMENT ME!
  - idcodeString
```
private java.lang.String idcodeString
```
    DOCUMENT ME!
  - idcodeWarpParentString
```
private java.lang.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 java.lang.String label1String
```
    DOCUMENT ME!
  - label2String
```
private java.lang.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 java.lang.String[] marksHelpString
```
    DOCUMENT ME!
  - marksLabString
```
private java.lang.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 java.lang.String noteDate001String
```
    DOCUMENT ME!
  - noteDate002String
```
private java.lang.String noteDate002String
```
    DOCUMENT ME!
  - noteDate003String
```
private java.lang.String noteDate003String
```
    DOCUMENT ME!
  - noteDate004String
```
private java.lang.String noteDate004String
```
    DOCUMENT ME!
  - noteDate005String
```
private java.lang.String noteDate005String
```
    DOCUMENT ME!
  - noteNumber001String
```
private java.lang.String noteNumber001String
```
    DOCUMENT ME!
  - noteNumber002String
```
private java.lang.String noteNumber002String
```
    DOCUMENT ME!
  - noteNumber003String
```
private java.lang.String noteNumber003String
```
    DOCUMENT ME!
  - noteNumber004String
```
private java.lang.String noteNumber004String
```
    DOCUMENT ME!
  - noteNumber005String
```
private java.lang.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 java.lang.String originalFileName
```
    DOCUMENT ME!
  - origName
```
private java.lang.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 java.lang.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 java.lang.String typeString
```
    DOCUMENT ME!
  - typeStringType
```
private int typeStringType
```
    DOCUMENT ME!
  - UI
```
private ViewUserInterface UI
```
    DOCUMENT ME!
  - viewType
```
private int viewType
```
    DOCUMENT ME!
  - volregBaseIdcodeString
```
private java.lang.String volregBaseIdcodeString
```
    DOCUMENT ME!
  - volregBaseNameString
```
private java.lang.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 java.lang.String volregGridparentIdcodeString
```
    DOCUMENT ME!
  - volregGridparentNameString
```
private java.lang.String volregGridparentNameString
```
    DOCUMENT ME!
  - volregInputIdcodeString
```
private java.lang.String volregInputIdcodeString
```
    DOCUMENT ME!
  - volregInputNameString
```
private java.lang.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 java.lang.String volregRotparentIdcodeString
```
    DOCUMENT ME!
  - volregRotparentNameString
```
private java.lang.String volregRotparentNameString
```
    DOCUMENT ME!
  - warpData
```
private float[] warpData
```
    DOCUMENT ME!
  - warpParentnameString
```
private java.lang.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 Detail
  - FileAfni
```
public FileAfni(java.lang.String fileName,
                java.lang.String fileDir,
                boolean loadB,
                boolean doRead)
         throws java.io.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:
    
    java.io.IOException - if there is an error making the file
- Method Detail
  - 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 java.io.IOException
```
    readImage.
    
    Returns:
    
    returns the image
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - setFileName
```
public void setFileName(java.lang.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 java.io.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:
    
    java.io.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 java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readHeader
```
public boolean readHeader()
                   throws java.io.IOException
```
    Reads AFNI header (.HEAD file)
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readImage2
```
private ModelImage readImage2()
                       throws java.io.IOException
```
    Reads AFNI image (.BRIK file)
    
    Returns:
    
    Generated modelImage
    
    Throws:
    
    java.io.IOException - data reading problem occured
  - readLine
```
private java.lang.String readLine()
                           throws java.io.IOException
```
    readLine() - reads a line of the file and strips comments indicated by the # symbol.
    
    Returns:
    
    the line read in
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readXYZBuffer
```
public void readXYZBuffer(int slice,
                          float[] buffer,
                          float[] dicomBuffer,
                          float scaleFact)
                   throws java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - removeWhiteSpace
```
private java.lang.String removeWhiteSpace(java.lang.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!

Class FileAfni

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

INTEGER_ATTRIBUTE

FLOAT_ATTRIBUTE

STRING_ATTRIBUTE

ANAT_SPGR_TYPE

ANAT_FSE_TYPE

ANAT_EPI_TYPE

ANAT_MRAN_TYPE

ANAT_CT_TYPE

ANAT_SPECT_TYPE

ANAT_PET_TYPE

ANAT_MRA_TYPE

ANAT_BMAP_TYPE

ANAT_DIFF_TYPE

ANAT_OMRI_TYPE

ANAT_BUCK_TYPE

FUNC_FIM_TYPE

FUNC_THR_TYPE

FUNC_COR_TYPE

FUNC_TT_TYPE

FUNC_FT_TYPE

FUNC_ZT_TYPE

FUNC_CT_TYPE

FUNC_BT_TYPE

FUNC_BN_TYPE

FUNC_GT_TYPE

FUNC_PT_TYPE

FUNC_BUCK_TYPE

FUNC_THR_SCALE_SHORT

FUNC_COR_SCALE_SHORT

FUNC_TT_SCALE_SHORT

FUNC_FT_SCALE_SHORT

FUNC_ZT_SCALE_SHORT

FUNC_CT_SCALE_SHORT

FUNC_BT_SCALE_SHORT

FUNC_BN_SCALE_SHORT

FUNC_GT_SCALE_SHORT

FUNC_PT_SCALE_SHORT

FUNC_THR_SCALE_BYTE

FUNC_COR_SCALE_BYTE

FUNC_TT_SCALE_BYTE

FUNC_ZT_SCALE_BYTE

FUNC_BT_SCALE_BYTE

FUNC_GT_SCALE_BYTE

MARKSET_ALIGN

MARKSET_BOUNDING

WARP_AFFINE_TYPE

WARP_TALAIRACH_12_TYPE

UNITS_MSEC_TYPE

UNITS_SEC_TYPE

UNITS_HZ_TYPE

ATLAS_FRONT_TO_AC

ATLAS_PC_TO_BACK

ATLAS_BOT_TO_AC

ATLAS_AC_TO_TOP

ATLAS_AC_TO_LAT

acpcAC

acpcMaxPt

acpcMinPt

acpcName

acpcPC

acpcRes

acquisitionDuration

alsoAcpc

alsoOrig

anatomyParentnameString

anatType

anotherPtDicom

brickFloatFacs

brickKeywordsString

brickLabsString

brickStatAux

brickStats