interfaces.camino.convert¶
AnalyzeHeader¶
Wraps command analyzeheader
Create or read an Analyze 7.5 header file.
Analyze image header, provides support for the most common header fields. Some fields, such as patient_id, are not currently supported. The program allows three nonstandard options: the field image_dimension.funused1 is the image scale. The intensity of each pixel in the associated .img file is (image value from file) * scale. Also, the origin of the Talairach coordinates (midline of the anterior commisure) are encoded in the field data_history.originator. These changes are included for compatibility with SPM.
All headers written with this program are big endian by default.
Example¶
>>> import nipype.interfaces.camino as cmon
>>> hdr = cmon.AnalyzeHeader()
>>> hdr.inputs.in_file = 'tensor_fitted_data.Bdouble'
>>> hdr.inputs.scheme_file = 'A.scheme'
>>> hdr.inputs.data_dims = [256,256,256]
>>> hdr.inputs.voxel_dims = [1,1,1]
>>> hdr.run()
Inputs:
[Mandatory]
datatype: (u'byte' or u'char' or u'[u]short' or u'[u]int' or u'float'
or u'complex' or u'double')
The char datatype is 8 bit (not the 16 bit char of Java), as
specified by the Analyze 7.5 standard. The byte, ushort and uint
types are not part of the Analyze specification but are supported by
SPM.
flag: -datatype %s
in_file: (an existing file name)
Tensor-fitted data filename
flag: < %s, position: 1
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
centre: (a list of from 3 to 3 items which are an integer (int or
long))
Voxel specifying origin of Talairach coordinate system for SPM,
default [0 0 0].
flag: -centre %s
data_dims: (a list of from 3 to 3 items which are an integer (int or
long))
data dimensions in voxels
flag: -datadims %s
description: (a string)
Short description - No spaces, max length 79 bytes. Will be null
terminated automatically.
flag: -description %s
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
greylevels: (a list of from 2 to 2 items which are an integer (int or
long))
Minimum and maximum greylevels. Stored as shorts in the header.
flag: -gl %s
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
initfromheader: (an existing file name)
Reads header information from file and intializes a new header with
the values read from the file. You may replace any combination of
fields in the new header by specifying subsequent options.
flag: -initfromheader %s, position: 3
intelbyteorder: (a boolean)
Write header in intel byte order (little-endian).
flag: -intelbyteorder
networkbyteorder: (a boolean)
Write header in network byte order (big-endian). This is the default
for new headers.
flag: -networkbyteorder
nimages: (an integer (int or long))
Number of images in the img file. Default 1.
flag: -nimages %d
offset: (an integer (int or long))
According to the Analyze 7.5 standard, this is the byte offset in
the .img file at which voxels start. This value can be negative to
specify that the absolute value is applied for every image in the
file.
flag: -offset %d
out_file: (a file name)
flag: > %s, position: -1
picoseed: (a list of from 3 to 3 items which are an integer (int or
long))
Voxel specifying the seed (for PICo maps), default [0 0 0].
flag: -picoseed %s
printbigendian: (an existing file name)
Prints 1 if the header is big-endian, 0 otherwise.
flag: -printbigendian %s, position: 3
printimagedims: (an existing file name)
Prints image data and voxel dimensions as Camino arguments and
exits.
flag: -printimagedims %s, position: 3
printintelbyteorder: (an existing file name)
Prints 1 if the header is little-endian, 0 otherwise.
flag: -printintelbyteorder %s, position: 3
printprogargs: (an existing file name)
Prints data dimension (and type, if relevant) arguments for a
specific Camino program, where prog is one of shredder,
scanner2voxel, vcthreshselect, pdview, track.
flag: -printprogargs %s, position: 3
readheader: (an existing file name)
Reads header information from file and prints to stdout. If this
option is not specified, then the program writes a header based on
the other arguments.
flag: -readheader %s, position: 3
scaleinter: (a float)
Constant to add to the image intensities. Used by SPM and MRIcro.
flag: -scaleinter %d
scaleslope: (a float)
Intensities in the image are scaled by this factor by SPM and
MRICro. Default is 1.0.
flag: -scaleslope %d
scheme_file: (an existing file name)
Camino scheme file (b values / vectors, see camino.fsl2scheme)
flag: %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
voxel_dims: (a list of from 3 to 3 items which are a float)
voxel dimensions in mm
flag: -voxeldims %s
Outputs:
header: (an existing file name)
Analyze header
DT2NIfTI¶
Wraps command dt2nii
Converts camino tensor data to NIfTI format
Reads Camino diffusion tensors, and converts them to NIFTI format as three .nii files.
Inputs:
[Mandatory]
header_file: (an existing file name)
A Nifti .nii or .hdr file containing the header information
flag: -header %s, position: 3
in_file: (an existing file name)
tract file
flag: -inputfile %s, position: 1
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
output_root: (a file name)
filename root prepended onto the names of three output files.
flag: -outputroot %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
dt: (an existing file name)
diffusion tensors in NIfTI format
exitcode: (an existing file name)
exit codes from Camino reconstruction in NIfTI format
lns0: (an existing file name)
estimated lns0 from Camino reconstruction in NIfTI format
Image2Voxel¶
Wraps command image2voxel
Converts Analyze / NIFTI / MHA files to voxel order.
Converts scanner-order data in a supported image format to voxel-order data. Either takes a 4D file (all measurements in single image) or a list of 3D images.
Examples¶
>>> import nipype.interfaces.camino as cmon
>>> img2vox = cmon.Image2Voxel()
>>> img2vox.inputs.in_file = '4d_dwi.nii'
>>> img2vox.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
4d image file
flag: -4dimage %s, position: 1
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
out_file: (a file name)
flag: > %s, position: -1
out_type: (u'float' or u'char' or u'short' or u'int' or u'long' or
u'double', nipype default value: float)
"i.e. Bfloat". Can be "char", "short", "int", "long", "float" or
"double"
flag: -outputdatatype %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
voxel_order: (an existing file name)
path/name of 4D volume in voxel order
NIfTIDT2Camino¶
Wraps command niftidt2camino
Converts NIFTI-1 diffusion tensors to Camino format. The program reads the NIFTI header but does not apply any spatial transformations to the data. The NIFTI intensity scaling parameters are applied.
The output is the tensors in Camino voxel ordering: [exit, ln(S0), dxx, dxy, dxz, dyy, dyz, dzz].
The exit code is set to 0 unless a background mask is supplied, in which case the code is 0 in brain voxels and -1 in background voxels.
The value of ln(S0) in the output is taken from a file if one is supplied, otherwise it is set to 0.
NOTE FOR FSL USERS - FSL’s dtifit can output NIFTI tensors, but they are not stored in the usual way (which is using NIFTI_INTENT_SYMMATRIX). FSL’s tensors follow the ITK / VTK “upper-triangular” convention, so you will need to use the -uppertriangular option to convert these correctly.
Inputs:
[Mandatory]
in_file: (an existing file name)
A NIFTI-1 dataset containing diffusion tensors. The tensors are
assumed to be in lower-triangular order as specified by the NIFTI
standard for the storage of symmetric matrices. This file should be
either a .nii or a .hdr file.
flag: -inputfile %s, position: 1
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
bgmask: (an existing file name)
Binary valued brain / background segmentation, may be a raw binary
file (specify type with -maskdatatype) or a supported image file.
flag: -bgmask %s
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
lns0_file: (an existing file name)
File containing the log of the unweighted signal for each voxel, may
be a raw binary file (specify type with -inputdatatype) or a
supported image file.
flag: -lns0 %s
out_file: (a file name)
flag: > %s, position: -1
s0_file: (an existing file name)
File containing the unweighted signal for each voxel, may be a raw
binary file (specify type with -inputdatatype) or a supported image
file.
flag: -s0 %s
scaleinter: (a float)
A value v in the diffusion tensor is scaled to v * s + i. This is
applied after any scaling specified by the input image. Default is
0.0.
flag: -scaleinter %s
scaleslope: (a float)
A value v in the diffusion tensor is scaled to v * s + i. This is
applied after any scaling specified by the input image. Default is
1.0.
flag: -scaleslope %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
uppertriangular: (a boolean)
Specifies input in upper-triangular (VTK style) order.
flag: -uppertriangular %s
Outputs:
out_file: (a file name)
diffusion tensors data in Camino format
ProcStreamlines¶
Wraps command procstreamlines
Process streamline data
- This program does post-processing of streamline output from track. It can either output streamlines or connection probability maps.
Examples¶
>>> import nipype.interfaces.camino as cmon
>>> proc = cmon.ProcStreamlines()
>>> proc.inputs.in_file = 'tract_data.Bfloat'
>>> proc.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
data file
flag: -inputfile %s, position: 1
[Optional]
allowmultitargets: (a boolean)
Allows streamlines to connect to multiple target volumes.
flag: -allowmultitargets
args: (a unicode string)
Additional parameters to the command
flag: %s
datadims: (a list of from 3 to 3 items which are an integer (int or
long))
data dimensions in voxels
flag: -datadims %s
directional: (a list of from 3 to 3 items which are an integer (int
or long))
Splits the streamlines at the seed point and computes separate
connection probabilities for each segment. Streamline segments are
grouped according to their dot product with the vector (X, Y, Z).
The ideal vector will be tangential to the streamline trajectory at
the seed, such that the streamline projects from the seed along (X,
Y, Z) and -(X, Y, Z). However, it is only necessary for the
streamline trajectory to not be orthogonal to (X, Y, Z).
flag: -directional %s
discardloops: (a boolean)
This option allows streamlines to enter a waypoint exactly once.
After the streamline leaves the waypoint, the entire streamline is
discarded upon a second entry to the waypoint.
flag: -discardloops
endpointfile: (a file name)
Image containing endpoint ROIs. This should be an Analyze 7.5 header
/ image file.hdr and file.img.
flag: -endpointfile %s
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
exclusionfile: (a file name)
Image containing exclusion ROIs. This should be an Analyze 7.5
header / image file.hdr and file.img.
flag: -exclusionfile %s
gzip: (a boolean)
save the output image in gzip format
flag: -gzip
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inputmodel: (u'raw' or u'voxels', nipype default value: raw)
input model type (raw or voxels)
flag: -inputmodel %s
iterations: (a float)
Number of streamlines generated for each seed. Not required when
outputting streamlines, but needed to create PICo images. The
default is 1 if the output is streamlines, and 5000 if the output is
connection probability images.
flag: -iterations %d
maxtractlength: (an integer (int or long))
maximum length of tracts
flag: -maxtractlength %d
maxtractpoints: (an integer (int or long))
maximum number of tract points
flag: -maxtractpoints %d
mintractlength: (an integer (int or long))
minimum length of tracts
flag: -mintractlength %d
mintractpoints: (an integer (int or long))
minimum number of tract points
flag: -mintractpoints %d
noresample: (a boolean)
Disables resampling of input streamlines. Resampling is
automatically disabled if the input model is voxels.
flag: -noresample
out_file: (a file name)
flag: > %s, position: -1
outputacm: (a boolean)
output all tracts in a single connection probability map (Analyze
image)
flag: -outputacm
requires: outputroot, seedfile
outputcbs: (a boolean)
outputs connectivity-based segmentation maps; requires target
outputfile
flag: -outputcbs
requires: outputroot, targetfile, seedfile
outputcp: (a boolean)
output the connection probability map (Analyze image, float)
flag: -outputcp
requires: outputroot, seedfile
outputroot: (a file name)
Prepended onto all output file names.
flag: -outputroot %s
outputsc: (a boolean)
output the connection probability map (raw streamlines, int)
flag: -outputsc
requires: outputroot, seedfile
outputtracts: (a boolean)
Output streamlines in raw binary format.
flag: -outputtracts
regionindex: (an integer (int or long))
index of specific region to process
flag: -regionindex %d
resamplestepsize: (a float)
Each point on a streamline is tested for entry into target,
exclusion or waypoint volumes. If the length between points on a
tract is not much smaller than the voxel length, then streamlines
may pass through part of a voxel without being counted. To avoid
this, the program resamples streamlines such that the step size is
one tenth of the smallest voxel dimension in the image. This
increases the size of raw or oogl streamline output and incurs some
performance penalty. The resample resolution can be controlled with
this option or disabled altogether by passing a negative step size
or by passing the -noresample option.
flag: -resamplestepsize %d
seedfile: (a file name)
Image Containing Seed Points
flag: -seedfile %s
seedpointmm: (a list of from 3 to 3 items which are an integer (int
or long))
The coordinates of a single seed point for tractography in mm
flag: -seedpointmm %s
seedpointvox: (a list of from 3 to 3 items which are an integer (int
or long))
The coordinates of a single seed point for tractography in voxels
flag: -seedpointvox %s
targetfile: (a file name)
Image containing target volumes.
flag: -targetfile %s
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
truncateinexclusion: (a boolean)
Retain segments of a streamline before entry to an exclusion ROI.
flag: -truncateinexclusion
truncateloops: (a boolean)
This option allows streamlines to enter a waypoint exactly once.
After the streamline leaves the waypoint, it is truncated upon a
second entry to the waypoint.
flag: -truncateloops
voxeldims: (a list of from 3 to 3 items which are an integer (int or
long))
voxel dimensions in mm
flag: -voxeldims %s
waypointfile: (a file name)
Image containing waypoints. Waypoints are defined as regions of the
image with the same intensity, where 0 is background and any value >
0 is a waypoint.
flag: -waypointfile %s
Outputs:
outputroot_files: (a list of items which are an existing file name)
proc: (an existing file name)
Processed Streamlines
Shredder¶
Wraps command shredder
Extracts periodic chunks from a data stream.
Shredder makes an initial offset of offset bytes. It then reads and outputs chunksize bytes, skips space bytes, and repeats until there is no more input.
If the chunksize is negative, chunks of size chunksize are read and the byte ordering of each chunk is reversed. The whole chunk will be reversed, so the chunk must be the same size as the data type, otherwise the order of the values in the chunk, as well as their endianness, will be reversed.
Examples¶
>>> import nipype.interfaces.camino as cam
>>> shred = cam.Shredder()
>>> shred.inputs.in_file = 'SubjectA.Bfloat'
>>> shred.inputs.offset = 0
>>> shred.inputs.chunksize = 1
>>> shred.inputs.space = 2
>>> shred.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
raw binary data file
flag: < %s, position: -2
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
chunksize: (an integer (int or long))
reads and outputs a chunk of chunksize bytes
flag: %d, position: 2
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
offset: (an integer (int or long))
initial offset of offset bytes
flag: %d, position: 1
out_file: (a file name)
flag: > %s, position: -1
space: (an integer (int or long))
skips space bytes
flag: %d, position: 3
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
shredded: (an existing file name)
Shredded binary data file
TractShredder¶
Wraps command tractshredder
Extracts bunches of streamlines.
tractshredder works in a similar way to shredder, but processes streamlines instead of scalar data. The input is raw streamlines, in the format produced by track or procstreamlines.
The program first makes an initial offset of offset tracts. It then reads and outputs a group of bunchsize tracts, skips space tracts, and repeats until there is no more input.
Examples¶
>>> import nipype.interfaces.camino as cmon
>>> shred = cmon.TractShredder()
>>> shred.inputs.in_file = 'tract_data.Bfloat'
>>> shred.inputs.offset = 0
>>> shred.inputs.bunchsize = 1
>>> shred.inputs.space = 2
>>> shred.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
tract file
flag: < %s, position: -2
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
bunchsize: (an integer (int or long))
reads and outputs a group of bunchsize tracts
flag: %d, position: 2
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
offset: (an integer (int or long))
initial offset of offset tracts
flag: %d, position: 1
out_file: (a file name)
flag: > %s, position: -1
space: (an integer (int or long))
skips space tracts
flag: %d, position: 3
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
Outputs:
shredded: (an existing file name)
Shredded tract file
VtkStreamlines¶
Wraps command vtkstreamlines
Use vtkstreamlines to convert raw or voxel format streamlines to VTK polydata
Examples¶
>>> import nipype.interfaces.camino as cmon
>>> vtk = cmon.VtkStreamlines()
>>> vtk.inputs.in_file = 'tract_data.Bfloat'
>>> vtk.inputs.voxeldims = [1,1,1]
>>> vtk.run()
Inputs:
[Mandatory]
in_file: (an existing file name)
data file
flag: < %s, position: -2
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
colourorient: (a boolean)
Each point on the streamline is coloured by the local orientation.
flag: -colourorient
environ: (a dictionary with keys which are a newbytes or None or a
newstr or None and with values which are a newbytes or None or a
newstr or None, nipype default value: {})
Environment variables
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
inputmodel: (u'raw' or u'voxels', nipype default value: raw)
input model type (raw or voxels)
flag: -inputmodel %s
interpolate: (a boolean)
the scalar value at each point on the streamline is calculated by
trilinear interpolation
flag: -interpolate
interpolatescalars: (a boolean)
the scalar value at each point on the streamline is calculated by
trilinear interpolation
flag: -interpolatescalars
out_file: (a file name)
flag: > %s, position: -1
scalar_file: (a file name)
image that is in the same physical space as the tracts
flag: -scalarfile %s, position: 3
seed_file: (a file name)
image containing seed points
flag: -seedfile %s, position: 1
target_file: (a file name)
image containing integer-valued target regions
flag: -targetfile %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
voxeldims: (a list of from 3 to 3 items which are an integer (int or
long))
voxel dimensions in mm
flag: -voxeldims %s, position: 4
Outputs:
vtk: (an existing file name)
Streamlines in VTK format