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interfaces.diffusion_toolkit.odf

HARDIMat

Link to code

Wraps command hardi_mat

Use hardi_mat to calculate a reconstruction matrix from a gradient table

Inputs:

[Mandatory]
bvals: (an existing file name)
        b values file
bvecs: (an existing file name)
        b vectors file
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
args: (a string)
        Additional parameters to the command
bvals: (an existing file name)
        b values file
bvecs: (an existing file name)
        b vectors file
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', 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
image_info: (an existing file name)
        specify image information file. the image info file is generated
         from original dicom image by diff_unpack program and contains image
         orientation and other information needed for reconstruction and
         tracking. by default will look into the image folder for .info file
image_orientation_vectors: (a list of from 6 to 6 items which are a
         float)
        specify image orientation vectors. if just one argument given,
         will treat it as filename and read the orientation vectors from
         the file. if 6 arguments are given, will treat them as 6 float
         numbers and construct the 1st and 2nd vector and calculate the 3rd
         one automatically.
         this information will be used to determine image orientation,
         as well as to adjust gradient vectors with oblique angle when
oblique_correction: (a boolean)
        when oblique angle(s) applied, some SIEMENS dti protocols do not
         adjust gradient accordingly, thus it requires adjustment for
        correct
         diffusion tensor calculation
odf_file: (an existing file name)
        filename that contains the reconstruction points on a HEMI-sphere.
         use the pre-set 181 points by default
order: (an integer)
        maximum order of spherical harmonics. must be even number. default
         is 4
out_file: (a file name, nipype default value: recon_mat.dat)
        output matrix file
reference_file: (an existing file name)
        provide a dicom or nifti image as the reference for the program to
         figure out the image orientation information. if no such info was
         found in the given image header, the next 5 options -info, etc.,
         will be used if provided. if image orientation info can be found
         in the given reference, all other 5 image orientation options will
         be IGNORED
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

out_file: (an existing file name)
        output matrix file

ODFRecon

Link to code

Wraps command odf_recon

Use odf_recon to generate tensors and other maps

Inputs:

[Mandatory]
DWI: (an existing file name)
        Input raw data
matrix: (an existing file name)
        use given file as reconstruction matrix.
n_b0: (an integer)
        number of b0 scans. by default the program gets this information
         from the number of directions and number of volumes in
         the raw data. useful when dealing with incomplete raw
         data set or only using part of raw data set to reconstruct
n_directions: (an integer)
        Number of directions
n_output_directions: (an integer)
        Number of output directions
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
DWI: (an existing file name)
        Input raw data
args: (a string)
        Additional parameters to the command
dsi: (a boolean)
        indicates that the data is dsi
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', nipype default value:
         {})
        Environment variables
filter: (a boolean)
        apply a filter (e.g. high pass) to the raw image
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
image_orientation_vectors: (a list of from 6 to 6 items which are a
         float)
        specify image orientation vectors. if just one argument given,
         will treat it as filename and read the orientation vectors from
         the file. if 6 arguments are given, will treat them as 6 float
         numbers and construct the 1st and 2nd vector and calculate the 3rd
         one automatically.
         this information will be used to determine image orientation,
         as well as to adjust gradient vectors with oblique angle when
matrix: (an existing file name)
        use given file as reconstruction matrix.
n_b0: (an integer)
        number of b0 scans. by default the program gets this information
         from the number of directions and number of volumes in
         the raw data. useful when dealing with incomplete raw
         data set or only using part of raw data set to reconstruct
n_directions: (an integer)
        Number of directions
n_output_directions: (an integer)
        Number of output directions
oblique_correction: (a boolean)
        when oblique angle(s) applied, some SIEMENS dti protocols do not
         adjust gradient accordingly, thus it requires adjustment for
        correct
         diffusion tensor calculation
out_prefix: (a string, nipype default value: odf)
        Output file prefix
output_entropy: (a boolean)
        output entropy map
output_type: ('nii' or 'analyze' or 'ni1' or 'nii.gz', nipype default
         value: nii)
        output file type
sharpness: (a float)
        smooth or sharpen the raw data. factor > 0 is smoothing.
         factor < 0 is sharpening. default value is 0
         NOTE: this option applies to DSI study only
subtract_background: (a boolean)
        subtract the background value before reconstruction
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

B0: (an existing file name)
DWI: (an existing file name)
ODF: (an existing file name)
entropy: (a file name)
max: (an existing file name)

ODFTracker

Link to code

Wraps command odf_tracker

Use odf_tracker to generate track file

Inputs:

[Mandatory]
ODF: (an existing file name)
mask1_file: (a file name)
        first mask image
max: (an existing file name)
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

[Optional]
ODF: (an existing file name)
angle_threshold: (a float)
        set angle threshold. default value is 35 degree for
         default tracking method and 25 for rk2
args: (a string)
        Additional parameters to the command
disc: (a boolean)
        use disc tracking
dsi: (a boolean)
         specify the input odf data is dsi. because dsi recon uses fixed
         pre-calculated matrix, some special orientation patch needs to
         be applied to keep dti/dsi/q-ball consistent.
environ: (a dictionary with keys which are a value of type 'str' and
         with values which are a value of type 'str', 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
image_orientation_vectors: (a list of from 6 to 6 items which are a
         float)
        specify image orientation vectors. if just one argument given,
         will treat it as filename and read the orientation vectors from
         the file. if 6 arguments are given, will treat them as 6 float
         numbers and construct the 1st and 2nd vector and calculate the 3rd
         one automatically.
         this information will be used to determine image orientation,
         as well as to adjust gradient vectors with oblique angle when
input_data_prefix: (a string, nipype default value: odf)
        recon data prefix
input_output_type: ('nii' or 'analyze' or 'ni1' or 'nii.gz', nipype
         default value: nii)
        input and output file type
invert_x: (a boolean)
        invert x component of the vector
invert_y: (a boolean)
        invert y component of the vector
invert_z: (a boolean)
        invert z component of the vector
limit: (an integer)
        in some special case, such as heart data, some track may go into
         infinite circle and take long time to stop. this option allows
         setting a limit for the longest tracking steps (voxels)
mask1_file: (a file name)
        first mask image
mask1_threshold: (a float)
        threshold value for the first mask image, if not given, the program
        will try automatically find the threshold
mask2_file: (a file name)
        second mask image
mask2_threshold: (a float)
        threshold value for the second mask image, if not given, the program
        will try automatically find the threshold
max: (an existing file name)
out_file: (a file name, nipype default value: tracks.trk)
        output track file
random_seed: (an integer)
        use random location in a voxel instead of the center of the voxel
         to seed. can also define number of seed per voxel. default is 1
runge_kutta2: (a boolean)
        use 2nd order runge-kutta method for tracking.
         default tracking method is non-interpolate streamline
slice_order: (an integer)
        set the slice order. 1 means normal, -1 means reversed. default
        value is 1
step_length: (a float)
        set step length, in the unit of minimum voxel size.
         default value is 0.1.
swap_xy: (a boolean)
        swap x and y vectors while tracking
swap_yz: (a boolean)
        swap y and z vectors while tracking
swap_zx: (a boolean)
        swap x and z vectors while tracking
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
        Control terminal output: `stream` - displays to terminal
        immediately, `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored
voxel_order: ('RAS' or 'RPS' or 'RAI' or 'RPI' or 'LAI' or 'LAS' or
         'LPS' or 'LPI')
        specify the voxel order in RL/AP/IS (human brain) reference. must be
         3 letters with no space in between.
         for example, RAS means the voxel row is from L->R, the column
         is from P->A and the slice order is from I->S.
         by default voxel order is determined by the image orientation
         (but NOT guaranteed to be correct because of various standards).
         for example, siemens axial image is LPS, coronal image is LIP and
         sagittal image is PIL.
         this information also is NOT needed for tracking but will be saved
         in the track file and is essential for track display to map onto
         the right coordinates

Outputs:

track_file: (an existing file name)
        output track file