interfaces.mrtrix3.preprocess¶
ResponseSD¶
Wraps command dwi2response
Estimate response function(s) for spherical deconvolution using the specified algorithm.
Example¶
>>> import nipype.interfaces.mrtrix3 as mrt
>>> resp = mrt.ResponseSD()
>>> resp.inputs.in_file = 'dwi.mif'
>>> resp.inputs.algorithm = 'tournier'
>>> resp.inputs.grad_fsl = ('bvecs', 'bvals')
>>> resp.cmdline
'dwi2response tournier -fslgrad bvecs bvals dwi.mif wm.txt'
>>> resp.run()
Inputs:
[Mandatory]
algorithm: ('msmt_5tt' or 'dhollander' or 'tournier' or 'tax')
response estimation algorithm (multi-tissue)
flag: %s, position: 1
in_file: (an existing file name)
input DWI image
flag: %s, position: -5
[Optional]
args: (a unicode string)
Additional parameters to the command
flag: %s
bval_scale: ('yes' or 'no')
specifies whether the b - values should be scaled by the square of
the corresponding DW gradient norm, as often required for multishell
or DSI DW acquisition schemes. The default action can also be set in
the MRtrix config file, under the BValueScaling entry. Valid choices
are yes / no, true / false, 0 / 1 (default: true).
flag: -bvalue_scaling %s
csf_file: (a file name)
output CSF response text file
flag: %s, position: -1
environ: (a dictionary with keys which are a bytes or None or a value
of class 'str' and with values which are a bytes or None or a value
of class 'str', nipype default value: {})
Environment variables
gm_file: (a file name)
output GM response text file
flag: %s, position: -2
grad_file: (an existing file name)
dw gradient scheme (MRTrix format
flag: -grad %s
grad_fsl: (a tuple of the form: (an existing file name, an existing
file name))
(bvecs, bvals) dw gradient scheme (FSL format
flag: -fslgrad %s %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
in_bval: (an existing file name)
bvals file in FSL format
in_bvec: (an existing file name)
bvecs file in FSL format
flag: -fslgrad %s %s
in_mask: (an existing file name)
provide initial mask image
flag: -mask %s
max_sh: (an integer (int or long))
maximum harmonic degree of response function
flag: -lmax %d
mtt_file: (a file name)
input 5tt image
flag: %s, position: -4
nthreads: (an integer (int or long))
number of threads. if zero, the number of available cpus will be
used
flag: -nthreads %d
terminal_output: ('stream' or 'allatonce' or 'file' or '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
wm_file: (a file name, nipype default value: wm.txt)
output WM response text file
flag: %s, position: -3
Outputs:
csf_file: (a file name)
output CSF response text file
flag: %s
gm_file: (a file name)
output GM response text file
flag: %s
wm_file: (a file name)
output WM response text file
flag: %s