A B C D E F G I M N P Q R S T V W X Y Z

A

ANZ_DAT_EXT - Static variable in class Nifti1Dataset

ANZ_HDR_EXT - Static variable in class Nifti1Dataset

ANZ_HDR_SIZE - Static variable in class Nifti1Dataset

ANZ_MAGIC_STRING - Static variable in class Nifti1Dataset

addExtension(int, String) - Method in class Nifti1Dataset

Add an extension stored in a file to a header

aux_file - Variable in class Nifti1Dataset

B

big_endian - Variable in class Nifti1Dataset

bytesPerVoxel(short) - Method in class Nifti1Dataset

Return bytes per voxel for each nifti-1 datatype

C

cal_max - Variable in class Nifti1Dataset

cal_min - Variable in class Nifti1Dataset

checkHeader() - Method in class Nifti1Dataset

Check the header fields for valid settings

copyHeader(Nifti1Dataset) - Method in class Nifti1Dataset

D

DIM5 - Variable in class Nifti1Dataset

DIM6 - Variable in class Nifti1Dataset

DIM7 - Variable in class Nifti1Dataset

DT_ALL - Static variable in class Nifti1Dataset

DT_BINARY - Static variable in class Nifti1Dataset

DT_NONE - Static variable in class Nifti1Dataset

data_type_string - Variable in class Nifti1Dataset

db_name - Variable in class Nifti1Dataset

decodeDatatype(short) - Method in class Nifti1Dataset

Decode the nifti datatype codes

decodeIntent(short) - Method in class Nifti1Dataset

Decode the nifti intent codes

decodeSliceOrder(short) - Method in class Nifti1Dataset

Decode the nifti slice order codes

decodeUnits(short) - Method in class Nifti1Dataset

Decode the nifti unit codes

decodeXform(short) - Method in class Nifti1Dataset

Decode the nifti xform codes

descrip - Variable in class Nifti1Dataset

dim_info - Variable in class Nifti1Dataset

ds_is_nii - Variable in class Nifti1Dataset

E

EXT_KEY_SIZE - Static variable in class Nifti1Dataset

EndianCorrectInputStream - class EndianCorrectInputStream.

EndianCorrectInputStream extends DataInputStream; it will optionally flip bytes to read little endian data correctly.

EndianCorrectInputStream(String, boolean) - Constructor for class EndianCorrectInputStream

Constructor for a disk file.

EndianCorrectInputStream(InputStream, boolean) - Constructor for class EndianCorrectInputStream

Constructor for an InputStream.

EndianCorrectOutputStream - class EndianCorrectOutputStream.

EndianCorrectOutputStream extends DataOutputStream; it will optionally flip bytes to write little endian data correctly.

EndianCorrectOutputStream(String, boolean) - Constructor for class EndianCorrectOutputStream

Constructor for a disk file.

EndianCorrectOutputStream(OutputStream, boolean) - Constructor for class EndianCorrectOutputStream

Constructor for an OutputStream.

exists() - Method in class Nifti1Dataset

Check if a valid dataset (header+data) exists.

existsDat() - Method in class Nifti1Dataset

Check if a valid dataset data file exists.

existsHdr() - Method in class Nifti1Dataset

Check if a valid dataset header file exists.

extension - Variable in class Nifti1Dataset

extents - Variable in class Nifti1Dataset

F

flipDouble(double) - Method in class EndianCorrectInputStream

flipDouble will flip the byte order of a double

flipDouble(double) - Method in class EndianCorrectOutputStream

flipDouble will flip the byte order of a double

flipFloat(float) - Method in class EndianCorrectInputStream

flipFloat will flip the byte order of a float

flipFloat(float) - Method in class EndianCorrectOutputStream

flipFloat will flip the byte order of a float

flipInt(int) - Method in class EndianCorrectInputStream

flipInt will flip the byte order of an int

flipInt(int) - Method in class EndianCorrectOutputStream

flipInt will flip the byte order of an int

flipLong(long) - Method in class EndianCorrectInputStream

flipLong will flip the byte order of a long

flipLong(long) - Method in class EndianCorrectOutputStream

flipLong will flip the byte order of a long

flipShort(short) - Method in class EndianCorrectInputStream

flipShort will byte flip a short

flipShort(short) - Method in class EndianCorrectOutputStream

flipShort will byte flip a short

freq_dim - Variable in class Nifti1Dataset

G

GZIP_EXT - Static variable in class Nifti1Dataset

getBitpix() - Method in class Nifti1Dataset

Get the bitpix field

getDataFilename() - Method in class Nifti1Dataset

Get the filename for the dataset data file

getDatatype() - Method in class Nifti1Dataset

Get the dataset datatype.

getExtensionsList() - Method in class Nifti1Dataset

Get list of extensions and return it as nx2 array

getHeaderFilename() - Method in class Nifti1Dataset

Get the filename for the dataset header file

glmax - Variable in class Nifti1Dataset

glmin - Variable in class Nifti1Dataset

I

intent - Variable in class Nifti1Dataset

intent_code - Variable in class Nifti1Dataset

intent_name - Variable in class Nifti1Dataset

M

magic - Variable in class Nifti1Dataset

main(String[]) - Static method in class Nifti1Dataset

main routine is used only for testing

N

NI1_EXT - Static variable in class Nifti1Dataset

NIFTI_FIRST_STATCODE - Static variable in class Nifti1Dataset

NIFTI_INTENT_BETA - Static variable in class Nifti1Dataset

NIFTI_INTENT_BINOM - Static variable in class Nifti1Dataset

NIFTI_INTENT_CHI - Static variable in class Nifti1Dataset

NIFTI_INTENT_CHISQ - Static variable in class Nifti1Dataset

NIFTI_INTENT_CHISQ_NONC - Static variable in class Nifti1Dataset

NIFTI_INTENT_CORREL - Static variable in class Nifti1Dataset

NIFTI_INTENT_DISPVECT - Static variable in class Nifti1Dataset

NIFTI_INTENT_ESTIMATE - Static variable in class Nifti1Dataset

NIFTI_INTENT_EXTVAL - Static variable in class Nifti1Dataset

NIFTI_INTENT_FTEST - Static variable in class Nifti1Dataset

NIFTI_INTENT_FTEST_NONC - Static variable in class Nifti1Dataset

NIFTI_INTENT_GAMMA - Static variable in class Nifti1Dataset

NIFTI_INTENT_GENMATRIX - Static variable in class Nifti1Dataset

NIFTI_INTENT_INVGAUSS - Static variable in class Nifti1Dataset

NIFTI_INTENT_LABEL - Static variable in class Nifti1Dataset

NIFTI_INTENT_LAPLACE - Static variable in class Nifti1Dataset

NIFTI_INTENT_LOGISTIC - Static variable in class Nifti1Dataset

NIFTI_INTENT_NEURONAME - Static variable in class Nifti1Dataset

NIFTI_INTENT_NONE - Static variable in class Nifti1Dataset

NIFTI_INTENT_NORMAL - Static variable in class Nifti1Dataset

NIFTI_INTENT_POINTSET - Static variable in class Nifti1Dataset

NIFTI_INTENT_POISSON - Static variable in class Nifti1Dataset

NIFTI_INTENT_PVAL - Static variable in class Nifti1Dataset

NIFTI_INTENT_QUATERNION - Static variable in class Nifti1Dataset

NIFTI_INTENT_SYMMATRIX - Static variable in class Nifti1Dataset

NIFTI_INTENT_TRIANGLE - Static variable in class Nifti1Dataset

NIFTI_INTENT_TTEST - Static variable in class Nifti1Dataset

NIFTI_INTENT_TTEST_NONC - Static variable in class Nifti1Dataset

NIFTI_INTENT_UNIFORM - Static variable in class Nifti1Dataset

NIFTI_INTENT_VECTOR - Static variable in class Nifti1Dataset

NIFTI_INTENT_WEIBULL - Static variable in class Nifti1Dataset

NIFTI_INTENT_ZSCORE - Static variable in class Nifti1Dataset

NIFTI_LAST_STATCODE - Static variable in class Nifti1Dataset

NIFTI_SLICE_ALT_DEC - Static variable in class Nifti1Dataset

NIFTI_SLICE_ALT_INC - Static variable in class Nifti1Dataset

NIFTI_SLICE_SEQ_DEC - Static variable in class Nifti1Dataset

NIFTI_SLICE_SEQ_INC - Static variable in class Nifti1Dataset

NIFTI_TYPE_COMPLEX128 - Static variable in class Nifti1Dataset

NIFTI_TYPE_COMPLEX256 - Static variable in class Nifti1Dataset

NIFTI_TYPE_COMPLEX64 - Static variable in class Nifti1Dataset

NIFTI_TYPE_FLOAT128 - Static variable in class Nifti1Dataset

NIFTI_TYPE_FLOAT32 - Static variable in class Nifti1Dataset

NIFTI_TYPE_FLOAT64 - Static variable in class Nifti1Dataset

NIFTI_TYPE_INT16 - Static variable in class Nifti1Dataset

NIFTI_TYPE_INT32 - Static variable in class Nifti1Dataset

NIFTI_TYPE_INT64 - Static variable in class Nifti1Dataset

NIFTI_TYPE_INT8 - Static variable in class Nifti1Dataset

NIFTI_TYPE_RGB24 - Static variable in class Nifti1Dataset

NIFTI_TYPE_UINT16 - Static variable in class Nifti1Dataset

NIFTI_TYPE_UINT32 - Static variable in class Nifti1Dataset

NIFTI_TYPE_UINT64 - Static variable in class Nifti1Dataset

NIFTI_TYPE_UINT8 - Static variable in class Nifti1Dataset

NIFTI_UNITS_HZ - Static variable in class Nifti1Dataset

NIFTI_UNITS_METER - Static variable in class Nifti1Dataset

NIFTI_UNITS_MICRON - Static variable in class Nifti1Dataset

NIFTI_UNITS_MM - Static variable in class Nifti1Dataset

NIFTI_UNITS_MSEC - Static variable in class Nifti1Dataset

NIFTI_UNITS_PPM - Static variable in class Nifti1Dataset

NIFTI_UNITS_SEC - Static variable in class Nifti1Dataset

NIFTI_UNITS_UNKNOWN - Static variable in class Nifti1Dataset

NIFTI_UNITS_USEC - Static variable in class Nifti1Dataset

NIFTI_XFORM_ALIGNED_ANAT - Static variable in class Nifti1Dataset

NIFTI_XFORM_MNI_152 - Static variable in class Nifti1Dataset

NIFTI_XFORM_SCANNER_ANAT - Static variable in class Nifti1Dataset

NIFTI_XFORM_TALAIRACH - Static variable in class Nifti1Dataset

NIFTI_XFORM_UNKNOWN - Static variable in class Nifti1Dataset

NII_HDR_SIZE - Static variable in class Nifti1Dataset

NII_MAGIC_STRING - Static variable in class Nifti1Dataset

Nifti1Dataset - class Nifti1Dataset.

Nifti1Dataset is an API for reading/writing nifti-1 datasets.
The definitive nifti-1 specification is the nifti1.h file on the NIfTI DFWG website

Nifti1Dataset(String) - Constructor for class Nifti1Dataset

Constructor for a dataset existing on disk.

Nifti1Dataset() - Constructor for class Nifti1Dataset

Constructor for creation of a new dataset.

P

phase_dim - Variable in class Nifti1Dataset

pixdim - Variable in class Nifti1Dataset

printDoubleTmcrs(double[]) - Method in class Nifti1Dataset

Print a voxel timecourse to standard out.

printHeader() - Method in class Nifti1Dataset

Print header information to standard out.

Q

qfac - Variable in class Nifti1Dataset

qform_code - Variable in class Nifti1Dataset

qoffset - Variable in class Nifti1Dataset

quatern - Variable in class Nifti1Dataset

R

readData() - Method in class Nifti1Dataset

Read all the data into one byte array.

readDoubleCorrect() - Method in class EndianCorrectInputStream

readDoubleCorrect will return a double from the stream

readDoubleTmcrs(short, short, short) - Method in class Nifti1Dataset

Read one 1D timecourse from a 4D dataset, ie all T values for a given XYZ location.

readDoubleVol(short) - Method in class Nifti1Dataset

Read one 3D volume from disk and return it as 3D double array

readFloatCorrect() - Method in class EndianCorrectInputStream

readFloatCorrect will return a float from the stream

readHeader() - Method in class Nifti1Dataset

Read header information into memory

readIntCorrect() - Method in class EndianCorrectInputStream

readIntCorrect will return an int from the stream

readLongCorrect() - Method in class EndianCorrectInputStream

readLongCorrect will return a long from the stream

readShortCorrect() - Method in class EndianCorrectInputStream

readShortCorrect will return a short from the stream

regular - Variable in class Nifti1Dataset

removeExtension(int) - Method in class Nifti1Dataset

Remove an extension from a header

S

scl_inter - Variable in class Nifti1Dataset

scl_slope - Variable in class Nifti1Dataset

session_error - Variable in class Nifti1Dataset

setDataFilename(String) - Method in class Nifti1Dataset

Set the filename for the dataset data file

setDatatype(short) - Method in class Nifti1Dataset

Set the dataset datatype.

setDims(short, short, short, short, short, short, short, short) - Method in class Nifti1Dataset

Set the dataset dimensions

setHeaderFilename(String) - Method in class Nifti1Dataset

Set the filename for the dataset header file

sform_code - Variable in class Nifti1Dataset

sizeof_hdr - Variable in class Nifti1Dataset

slice_code - Variable in class Nifti1Dataset

slice_dim - Variable in class Nifti1Dataset

slice_duration - Variable in class Nifti1Dataset

slice_end - Variable in class Nifti1Dataset

slice_start - Variable in class Nifti1Dataset

srow_x - Variable in class Nifti1Dataset

srow_y - Variable in class Nifti1Dataset

srow_z - Variable in class Nifti1Dataset

T

TDIM - Variable in class Nifti1Dataset

t_unit_code - Variable in class Nifti1Dataset

toffset - Variable in class Nifti1Dataset

V

vox_offset - Variable in class Nifti1Dataset

W

writeData(byte[]) - Method in class Nifti1Dataset

Write a byte array of data to disk, starting at vox_offset, beginning of image data.

writeDoubleCorrect(double) - Method in class EndianCorrectOutputStream

writeDoubleCorrect will write a double to the stream

writeFloatCorrect(float) - Method in class EndianCorrectOutputStream

writeFloatCorrect will write a float to the stream

writeHeader() - Method in class Nifti1Dataset

Write header information to disk file

writeIntCorrect(int) - Method in class EndianCorrectOutputStream

writeIntCorrect will write an int to the stream

writeLongCorrect(long) - Method in class EndianCorrectOutputStream

writeLongCorrect will write a long to the stream

writeShortCorrect(short) - Method in class EndianCorrectOutputStream

writeShortCorrect will write a short to the stream

writeVol(double[][][], short) - Method in class Nifti1Dataset

Write one 3D double array to disk.

X

XDIM - Variable in class Nifti1Dataset

xyz_unit_code - Variable in class Nifti1Dataset

xyzt_units - Variable in class Nifti1Dataset

Y

YDIM - Variable in class Nifti1Dataset

Z

ZDIM - Variable in class Nifti1Dataset

A B C D E F G I M N P Q R S T V W X Y Z