com.xinapse.multisliceimage.Analyze
Class NIFTIHeader

java.lang.Object
  com.xinapse.multisliceimage.Analyze.ANZHeader
      com.xinapse.multisliceimage.Analyze.NIFTIHeader

All Implemented Interfaces:

java.lang.Cloneable

public class NIFTIHeader
extends ANZHeader

This class represents a multi-dimensional NIFTI image header file. The header file may either:

• contain all the dimensional and descriptive information about an Analyze image, but none of the pixel data. This is the conventional Analyze 7.5 .img/.hdr file format.
• contain both the the dimensional and descriptive information about an Analyze image, and also the pixel data. This is the new NIFTI .nii file format.

Field Summary

static boolean	DEFAULT_FSL_COMPATIBLE_NIFTI The default setting of whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
static boolean	DEFAULT_SAVE_FSL_ORIENT The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
static boolean	DEFAULT_SAVE_SPM_ORIENT The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
static java.lang.String	FSL_COMPATIBLE_NIFTI_PROPERTY_KEY The property value key for setting whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
NIFTIXForm	qForm The NIFTI qform parameter.
float	qOffsetX The NIFTI qoffset_x parameter.
float	qOffsetY The NIFTI qoffset_y parameter.
float	qOffsetZ The NIFTI qoffset_z parameter.
float	quaternB The NIFTI quatern_b parameter.
float	quaternC The NIFTI quatern_c parameter.
float	quaternD The NIFTI quatern_d parameter.
static java.lang.String	SAVE_FSL_ORIENT_PROPERTY_KEY The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
static java.lang.String	SAVE_SPM_ORIENT_PROPERTY_KEY The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
NIFTIXForm	sForm The NIFTI sform parameter.
float[]	sRowX The NIFTI srow_x parameter.
float[]	sRowY The NIFTI srow_y parameter.
float[]	sRowZ The NIFTI srow_z parameter.

Fields inherited from class com.xinapse.multisliceimage.Analyze.ANZHeader

COMPRESSED_EXTENSION, COMPRESSED_UPPERCASE_EXTENSION, EXTENSION, MAXDIM, UPPERCASE_EXTENSION, voxOffset

Method Summary

java.lang.Object	clone() Returns an exact copy of this NIFTI header.
protected void	finalize() Called by the garbage collector on this NIFTIHeader when garbage collection determines that there are no more references to the header.
static boolean	getPreferredFSLCompatibleNIFTI() Returns the user's preference about whether NIFTI-1 images with both qform and sform orientations unset should be read as having the patient left coordinate increasing with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.
static boolean	getPreferredSaveFSLOrient() Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
static boolean	getPreferredSaveSPMOrient() Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
static void	savePreferredFSLCompatibleNIFTI(boolean b) Saves the user's preference about whether NIFTI-1 images should be read as having the patient left coordinate increasing with stored pixel data column number.
static void	savePreferredSaveFSLOrient(boolean b) Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.
static void	savePreferredSaveSPMOrient(boolean b) Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.
void	setImageOrientationPositionPatient(javax.vecmath.Vector3f[] cosines, javax.vecmath.Point3f position)
java.lang.String	toString() Returns a String representation of this NIFTIHeader.
java.lang.String	toString(boolean html) Returns the string representation of this NIFTI-1 compliant image header, with optional presentation in HTML format.

Methods inherited from class com.xinapse.multisliceimage.Analyze.ANZHeader

getDBName, getDescription, getMinMax, setDBName, setDims, setMinMax, setNCols, setNFrames, setNRows, setNSlices

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

SAVE_FSL_ORIENT_PROPERTY_KEY

public static final java.lang.String SAVE_FSL_ORIENT_PROPERTY_KEY

The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.

See Also:

Constant Field Values

SAVE_SPM_ORIENT_PROPERTY_KEY

public static final java.lang.String SAVE_SPM_ORIENT_PROPERTY_KEY

The property value key for setting whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.

See Also:

Constant Field Values

FSL_COMPATIBLE_NIFTI_PROPERTY_KEY

public static final java.lang.String FSL_COMPATIBLE_NIFTI_PROPERTY_KEY

The property value key for setting whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.

See Also:

Constant Field Values

DEFAULT_SAVE_FSL_ORIENT

public static final boolean DEFAULT_SAVE_FSL_ORIENT

The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.

See Also:

Constant Field Values

DEFAULT_SAVE_SPM_ORIENT

public static final boolean DEFAULT_SAVE_SPM_ORIENT

The default setting of whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.

See Also:

Constant Field Values

DEFAULT_FSL_COMPATIBLE_NIFTI

public static final boolean DEFAULT_FSL_COMPATIBLE_NIFTI

The default setting of whether NIFTI-1 images that have qform and sform orientation both unset should be read as having an increasing a patient left coordinate value with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information.

See Also:

Constant Field Values

qForm

public NIFTIXForm qForm

The NIFTI qform parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

sForm

public NIFTIXForm sForm

The NIFTI sform parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

quaternB

public float quaternB

The NIFTI quatern_b parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

quaternC

public float quaternC

The NIFTI quatern_c parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

quaternD

public float quaternD

The NIFTI quatern_d parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

qOffsetX

public float qOffsetX

The NIFTI qoffset_x parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

qOffsetY

public float qOffsetY

The NIFTI qoffset_y parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

qOffsetZ

public float qOffsetZ

The NIFTI qoffset_z parameter. It is not recommended to manipulate this directly. Use the methods to set the image position and orientation in NIFTImage.

sRowX

public float[] sRowX

The NIFTI srow_x parameter. This is usually set using the method setSFormAffineTransform of the NIFTImage.

sRowY

public float[] sRowY

The NIFTI srow_y parameter. This is usually set using the method setSFormAffineTransform of the NIFTImage.

sRowZ

public float[] sRowZ

The NIFTI srow_z parameter. This is usually set using the method setSFormAffineTransform of the NIFTImage.

Method Detail

getPreferredSaveFSLOrient

public static boolean getPreferredSaveFSLOrient()

Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible. FSL is not able to correctly display images with an orientation that is not in the expected orientation. If interoperating with FSL, it may be necessary to save images in an FSL-friendly orientation. If not set in the user's preferences, then the default is to save NIFTI-1 images with a radiological orientation.

If the system property "analyze.fslorient" exists, and the property value is either "true" or "false", then the user's preference is overridden by the property value.

Returns:

whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.

savePreferredSaveFSLOrient

public static void savePreferredSaveFSLOrient(boolean b)

Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with FSL, where possible.

Parameters:

b - true if NIFTI-1 images should have an orientation that is compatible with FSL, where possible; false otherwise.

getPreferredSaveSPMOrient

public static boolean getPreferredSaveSPMOrient()

Returns the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible. SPM is not able to correctly display images with an orientation that is not in the expected orientation. If interoperating with SPM, it may be necessary to save images in an SPM-friendly orientation. If not set in the user's preferences, then the default is to save NIFTI-1 images with a radiological orientation.

If the system property "analyze.spmorient" exists, and the property value is either "true" or "false", then the user's preference is overridden by the property value.

Returns:

whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.

savePreferredSaveSPMOrient

public static void savePreferredSaveSPMOrient(boolean b)

Saves the user's preference about whether NIFTI-1 images should be saved with an orientation that is compatible with SPM, where possible.

Parameters:

b - true if NIFTI-1 images should have an orientation that is compatible with SPM, where possible; false otherwise.

getPreferredFSLCompatibleNIFTI

public static boolean getPreferredFSLCompatibleNIFTI()

Returns the user's preference about whether NIFTI-1 images with both qform and sform orientations unset should be read as having the patient left coordinate increasing with stored pixel data column number, and whether NIFTI-1 images should be prevented from being written without orientation information. This may be necessary if interoperating with FSL.

If not set in the user's preferences, then the default is to interpret NIFTI-1 images as axial with an increasing patient right coordinate with increasing column number.

If the system property "nifti.fslcompatible" exists, and the property value is either "true" or "false", then the user's preference is overridden by the property value.

Returns:

whether NIFTI-1 images with both qform and sformunset should be interpreted as having an increasing left coordinate with stored pixel data column number.

savePreferredFSLCompatibleNIFTI

public static void savePreferredFSLCompatibleNIFTI(boolean b)

Saves the user's preference about whether NIFTI-1 images should be read as having the patient left coordinate increasing with stored pixel data column number.

Parameters:

b - true if NIFTI-1 images should be read as having the patient left coordinate increasing with stored pixel data column number; false otherwise.

finalize

protected void finalize()
                 throws java.lang.Throwable

Called by the garbage collector on this NIFTIHeader when garbage collection determines that there are no more references to the header.

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable - - the Exception raised by this method.

setImageOrientationPositionPatient

public void setImageOrientationPositionPatient(javax.vecmath.Vector3f[] cosines,
                                               javax.vecmath.Point3f position)
                                        throws MultiSliceImageException

Throws:

MultiSliceImageException

toString

public java.lang.String toString()

Returns a String representation of this NIFTIHeader.

Overrides:

toString in class ANZHeader

Returns:

a String describing this NIFTIHeader.

toString

public java.lang.String toString(boolean html)

Returns the string representation of this NIFTI-1 compliant image header, with optional presentation in HTML format.

Overrides:

toString in class ANZHeader

Parameters:

html - if true, then the string will contain HTML tags.

Returns:

a String describing the header, optionally in HTML format.

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Returns an exact copy of this NIFTI header.

Overrides:

clone in class ANZHeader

Returns:

an exact copy of this NIFTIHeader instance.

Throws:

java.lang.CloneNotSupportedException