preadNrrd.m File Reference

Functions
	elseif (foundKeyword('DWMRI_GRADIENT_', cs))[iGNr
	elseif (foundKeyword('DWMRI_B-VALUE', cs)) headerInfo.bvalue
	elseif (foundKeyword('MODALITY', cs)) headerInfo.modality
	elseif (foundKeyword('MEASUREMENT FRAME:', cs)) iMF
	elseif (foundKeyword('SPACE ORIGIN:', cs)) iSO
	elseif (foundKeyword('SPACE UNITS:', cs)) headerInfo.spaceunits
	elseif (foundKeyword('CENTERINGS:', cs)) headerInfo.centerings
	elseif (foundKeyword('KINDS:', cs)) headerInfo.kinds
	elseif (foundKeyword('THICKNESSES:', cs)) sThicknesses
	elseif (foundKeyword('SIZES:', cs)) iSizes
end	elseif (foundKeyword('SPACE DIRECTIONS:', cs))%in case of a tensor volume there are 4 dimensions
	elseif (foundKeyword('SPACE:', cs)) headerInfo.space
	elseif (foundKeyword('DIMENSION:', cs)) headerInfo.dimension
	elseif (foundKeyword('DATA FILE:', cs)) headerInfo.datafile
	elseif (foundKeyword('ENCODING:', cs)) headerInfo.encoding
	elseif (foundKeyword('ENDIAN:', cs)) headerInfo.endian
	elseif (foundKeyword('TYPE:', cs)) headerInfo.type
return	elseif (foundKeyword( 'CONTENT:', cs)) headerInfo.content
function	error (['Original measurement frame needed to transform tensor back into original measurement frame'])
	fprintf ('Type has not been adapted, your data type is not unsupported.\n')
otherwise	fprintf ('Unknown type:%s\n', headerInfo.type)
else	fprintf ('Warning:File is not RAS, make sure subsequent matlab processing is consistent!\n')
headerInfo	gradients (iGNr+1,:)
return end	if (strcmp(csU(1:lenKeyword), keyWordU)) fk
	if (len< lenKeyword) fk=0
else	if (~iLastWasDelimiter) indxList
	if (numDelimiters >=1) sl
	if (isempty(assgnLoc)) dwiGradient
	if (transformDT &strcmp(headerInfo.kinds(1),'3D-masked-symmetric-matrix')) headerInfo
return end	if (strcmp(headerInfo.kinds(1),'3D-masked-symmetric-matrix'))%assume tensor data%assumed default centerings for tenssor data
end	if (strcmp(headerInfo.data,'')==1) fprintf('No data.\n')
only implemented for RAS	if (iLocation >0) iIsRas
	if (strncmp(cs, 'No volume', 9)) fprintf('%s\n'
	iMF (3) iMF(6) iMF(9)]
	iMF (2) iMF(5) iMF(8)
	iSD (3) iSD(6) iSD(9)]
	iSD (2) iSD(5) iSD(8)
	while (iEnd >1 &strList(iEnd)==delim) iEnd
	while (iStart< len &strList(iStart)==delim) iStart
	while (~strcmp(cs, '')) csU
Variables
find where the assignment is	assgnLoc = strfind( st, ':=' )
headerInfo	centerings = [{'?^} {'cell'} {'cell'} {'cell'}]
	cs = pgetl(p)
else let s see if we are dealing with a comment	csTmp = removeExcessDelimiters( cs, ' ' )
assumed default space units for tenssor	data = '?^
	dataSize = prod(headerInfo.sizes)
	delimiterIndices = strfind(strList,' ')
headerInfo	dimension = '?^
	dwiGradient = extractGradient( cs(length('DWMRI_GRADIENT_')+1:end ) )
headerInfo	encoding = '?^
headerInfo	endian = '?^
return function	fk
default	header
function	headerInfo
end	iEnd = len
for	iI
end	iLastWasDelimiter = 0
	iLocation = strfind( csU(length('SPACE:')+1:end ), 'RIGHT-ANTERIOR-SUPERIOR')
end	indxList = []
return function	iNrs
	iSD = extractNumbersWithout( space_dir_tmp, {'(',')',','} )
	iStart = 1
	iThicknesses = []
	keyWordU = upper( keyWord )
tensor has to have headerInfo	kinds
end return function	kvs
	len = length( strList )
	lenKeyword = length( keyWord )
	lenThicknesses = length( sThicknesses )
end return helper functions from	marc
decided that the none is not needed in	matlab
headerInfo	measurementframe = [NaN NaN NaN
NaN NaN	NaN
	numDelimiters = length(delimiterIndices)
these fields are	optional
end Now read the data	popenType = nrrd2popenType( headerInfo.type )
	return
headerInfo	sizes = '?^
end return function	sl
headerInfo	space = '?^
end but only of them are in space	space_dir_tmp = strrep( cs(length('SPACE DIRECTIONS:')+1:end), 'none', 'NaN' )
headerInfo scalar data is expected to have values headerInfo	spacedirections = [NaN NaN NaN
headerInfo	spaceorigin = [NaN NaN NaN]
headerInfo	spaceunits = {'mm' 'mm' 'mm'}
headerInfo	thicknesses = iThicknesses
function	transformDT
headerInfo	type = '?^

---

Function Documentation

elseif

(

foundKeyword('DWMRI_GRADIENT_', cs)

)

elseif

(

foundKeyword('DWMRI_B-VALUE', cs)

)

elseif

(

foundKeyword('MODALITY', cs)

)

elseif

(

foundKeyword('MEASUREMENT FRAME:', cs)

)

elseif

(

foundKeyword('SPACE ORIGIN:', cs)

)

elseif

(

foundKeyword('SPACE UNITS:', cs)

)

elseif

(

foundKeyword('CENTERINGS:', cs)

)

elseif

(

foundKeyword('KINDS:', cs)

)

elseif

(

foundKeyword('THICKNESSES:', cs)

)

elseif

(

foundKeyword('SIZES:', cs)

)

end elseif

(

foundKeyword('SPACE DIRECTIONS:', cs)

)

elseif

(

foundKeyword('SPACE:', cs)

)

elseif

(

foundKeyword('DIMENSION:', cs)

)

elseif

(

foundKeyword('DATA FILE:', cs)

)

elseif

(

foundKeyword('ENCODING:', cs)

)

elseif

(

foundKeyword('ENDIAN:', cs)

)

elseif

(

foundKeyword('TYPE:', cs)

)

return elseif

(

foundKeyword( 'CONTENT:', cs)

)

function error

(

)

Type Constraints

Referenced by Cudapp::HostMemory::AllocateBytes(), Cudapp::DeviceMemory::AllocateBytes(), Cudapp::MemoryPitch::AllocatePitchBytes(), vtkSlicerParameterWidget::CreateWidgets(), endElement(), vtkPreciseHyperStreamline::Execute(), lmEndElement(), lmStartElement(), makeipaddr(), OpenGLBufferObject::Map(), vtkNeuroNavLogic::PerformPatientToImageRegistration(), vtkSlicerGPURayCastVolumeTextureMapper3D::PrintGLErrorString(), vtkSlicerGPURayCastVolumeMapper::PrintGLErrorString(), vtkSlicerGPURayCastMultiVolumeMapper::PrintGLErrorString(), qMRMLModelTest1(), qMRMLTransformProxyModelTest1(), vtkFSSurfaceAnnotationReader::ReadFSAnnotation(), ReadPGM(), OpenGLBufferObject::Register(), LoadableModuleFactory::ScanForSharedObjectModules(), setipaddr(), vtkSlicerModulesStep::SetStatus(), socket_getaddrinfo(), socket_getnameinfo(), startElement(), OpenGLBufferObject::Unmap(), and OpenGLBufferObject::Unregister().

fprintf	(	'Type has not been	adapted,
		your data type is not unsupported.\n'
	)

otherwise fprintf	(	'Unknown type:%s\n'	,
		headerInfo.	type
	)

else fprintf	(	'Warning:File is not	RAS,
		make sure subsequent matlab processing is consistent!\n'
	)

headerInfo gradients	(	iGNr+	1,
		:
	)

return end if

(

strcmp(csU(1:lenKeyword), keyWordU)

)

if

(

)

[pure virtual]

else if

(

~

iLastWasDelimiter

)

if

(

numDelimiters >=

1

)

References numDelimiters.

if

(

isempty(assgnLoc)

)

if

(

transformDT &

strcmpheaderInfo.kinds(1),'3D-masked-symmetric-matrix'

)

return end if

(

strcmp(headerInfo.kinds(1),'3D-masked-symmetric-matrix')

)

end if

(

strcmp(headerInfo.data,'')

= =1

)

only implemented for RAS if	(	iLocation	,
		0
	)

if

(

strncmp(cs, 'No volume', 9)

)

iMF

(

3

)

iMF

(

2

)

iSD

(

3

)

iSD

(

2

)

while	(	iEnd	,
		1 &	strListiEnd = =delim
	)

while

(

)

while

(

~

strcmpcs, ''

)

---

Variable Documentation

find where the assignment is assgnLoc = strfind( st, ':=' )

headerInfo centerings = [{'?^} {'cell'} {'cell'} {'cell'}]

if ( csTmp(1)~='#' & ~strcmp(cs(1:4),'NRRD') ) fprintf('Warning end end cs = pgetl(p)

Referenced by SlowFT2().

else let s see if we are dealing with a comment csTmp = removeExcessDelimiters( cs, ' ' )

headerInfo data = '?^

dataSize = prod(headerInfo.sizes)

delimiterIndices = strfind(strList,' ')

headerInfo dimension = '?^

else dwiGradient = extractGradient( cs(length('DWMRI_GRADIENT_')+1:end ) )

headerInfo encoding = '?^

headerInfo endian = '?^

return else fk

Initial value:

 foundKeyword( keyWord, cs )

csU = upper( cs )

default header

end clear headerInfo

Initial value:

 preadNrrd( p, transformDT, original_measurementframe )

% read a nrrd image from a pipe opened by popenr
% input: p pipe

end iEnd = len

for iI

Initial value:

1:lenThicknesses
      iThicknesses = [iThicknesses, str2num( sThicknesses{iI} ) ]

end iLastWasDelimiter = 0

iLocation = strfind( csU(length('SPACE:')+1:end ), 'RIGHT-ANTERIOR-SUPERIOR')

end indxList = []

end iNrs

Initial value:

 extractNumbersWithout( inputString, withoutTokens )

auxStr = inputString

iSD = extractNumbersWithout( space_dir_tmp, {'(',')',','} )

iStart = 1

iThicknesses = []

keyWordU = upper( keyWord )

headerInfo kinds

Initial value:

 [{'3D-masked-symmetric-matrix'} 
% {'space'} {'space'} {'space'}]

else kvs

Initial value:

 extractKeyValueString( st )

assgnLoc = strfind( st, ':=' )

len = length( strList )

lenKeyword = length( keyWord )

lenThicknesses = length( sThicknesses )

end return helper functions from marc

decided that the none is not needed in matlab

headerInfo measurementframe = [NaN NaN NaN

NaN NaN NaN

numDelimiters = length(delimiterIndices)

these fields are optional

end Now read the data popenType = nrrd2popenType( headerInfo.type )

return

parse sizes headerInfo sizes = '?^

end end sl

Initial value:

 extractStringList( strList )

strList = removeExcessDelimiters( strList, ' ' )

headerInfo space = '?^

decided that the none is not needed in it s nicer to have a matrix space_dir_tmp = strrep( cs(length('SPACE DIRECTIONS:')+1:end), 'none', 'NaN' )

if (length(iSD)~=9 & length(iSD)~=10) fprintf('Warning end headerInfo spacedirections = [NaN NaN NaN

if (length(iSO)~=3) % fprintf('Warning end headerInfo spaceorigin = [NaN NaN NaN]

headerInfo spaceunits = {'mm' 'mm' 'mm'}

end headerInfo thicknesses = iThicknesses

function transformDT

headerInfo type = '?^