interfaces.diffusion_toolkit.dti¶
DTIRecon¶
Wraps the executable command dti_recon
.
Use dti_recon to generate tensors and other maps
Inputs:
[Mandatory]
DWI: (an existing file name)
Input diffusion volume
argument: ``%s``, position: 1
bvecs: (an existing file name)
b vectors file
argument: ``-gm %s``
bvals: (an existing file name)
b values file
[Optional]
out_prefix: (a unicode string, nipype default value: dti)
Output file prefix
argument: ``%s``, position: 2
output_type: ('nii' or 'analyze' or 'ni1' or 'nii.gz', nipype default
value: nii)
output file type
argument: ``-ot %s``
n_averages: (an integer (int or long))
Number of averages
argument: ``-nex %s``
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
argument: ``-iop %f``
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
argument: ``-oc``
b0_threshold: (a float)
program will use b0 image with the given threshold to mask out high
background of fa/adc maps. by default it will calculate threshold
automatically. but if it failed, you need to set it manually.
argument: ``-b0_th``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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
Outputs:
ADC: (an existing file name)
B0: (an existing file name)
L1: (an existing file name)
L2: (an existing file name)
L3: (an existing file name)
exp: (an existing file name)
FA: (an existing file name)
FA_color: (an existing file name)
tensor: (an existing file name)
V1: (an existing file name)
V2: (an existing file name)
V3: (an existing file name)
DTITracker¶
Wraps the executable command dti_tracker
.
Inputs:
[Mandatory]
mask1_file: (a file name)
first mask image
argument: ``-m %s``, position: 2
[Optional]
tensor_file: (an existing file name)
reconstructed tensor file
input_type: ('nii' or 'analyze' or 'ni1' or 'nii.gz')
input and output file type. accepted values are:
analyze -> analyze format 7.5
ni1 -> nifti format saved in seperate .hdr and .img file
nii -> nifti format with one .nii file
nii.gz -> nifti format with compression
default type is 'nii'
argument: ``-it %s``
tracking_method: ('fact' or 'rk2' or 'tl' or 'sl')
fact -> use FACT method for tracking. this is the default method.
rk2 -> use 2nd order runge-kutta method for tracking.
tl -> use tensorline method for tracking.
sl -> use interpolated streamline method with fixed step-length
argument: ``-%s``
step_length: (a float)
set step length, in the unit of minimum voxel size.
default value is 0.5 for interpolated streamline method
and 0.1 for other methods
argument: ``-l %f``
angle_threshold: (a float)
set angle threshold. default value is 35 degree
argument: ``-at %f``
angle_threshold_weight: (a float)
set angle threshold weighting factor. weighting will be be applied
on top of the angle_threshold
argument: ``-atw %f``
random_seed: (an integer (int or long))
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
argument: ``-rseed %d``
invert_x: (a boolean)
invert x component of the vector
argument: ``-ix``
invert_y: (a boolean)
invert y component of the vector
argument: ``-iy``
invert_z: (a boolean)
invert z component of the vector
argument: ``-iz``
swap_xy: (a boolean)
swap x & y vectors while tracking
argument: ``-sxy``
swap_yz: (a boolean)
swap y & z vectors while tracking
argument: ``-syz``
swap_zx: (a boolean)
swap x & z vectors while tracking
argument: ``-szx``
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
argument: ``-m2 %s``, position: 4
mask2_threshold: (a float)
threshold value for the second mask image, if not given, the program
will try automatically find the threshold
input_data_prefix: (a unicode string, nipype default value: dti)
for internal naming use only
argument: ``%s``, position: 0
output_file: (a file name, nipype default value: tracks.trk)
argument: ``%s``, position: 1
output_mask: (a file name)
output a binary mask file in analyze format
argument: ``-om %s``
primary_vector: ('v2' or 'v3')
which vector to use for fibre tracking: v2 or v3. If not set use v1
argument: ``-%s``
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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
Outputs:
track_file: (an existing file name)
mask_file: (an existing file name)