Phybers
Functions
phybers.utils.utilities Namespace Reference

Functions

def deform (in_imgdef, indir, outdir)
 Transforms a tractography file to another space using a non-linear deformation file. More...
 
def sampling (indir, in_npoints, outdir)
 Fiber sampling at n equidistant points. More...
 
def inter2bundles (dir_fib1, dir_fib2, outdir, d_th)
 Calculates a similarity measure between two sets of brain fibers (fiber clusters or segmented bundles). More...
 
def postprocessing (in_directory)
 Contains a set of algorithms that are applied on the results of clustering and segmentation algorithms. More...
 
def write_bundle (outfile, points)
 Write bundles File.
 
def read_bundle (infile)
 Read Bundles File.
 

Detailed Description

The utils subpackage is a compendium of tools used for both the pre-processing of a tractography as well as for evaluating the performance of the clustering and the segmentation. It includes 4 modules:
    1) deform
    2) sampling
    3) intersection
    4) postprocessing

Function Documentation

◆ deform()

def phybers.utils.utilities.deform (   in_imgdef,
  indir,
  outdir 
)

Transforms a tractography file to another space using a non-linear deformation file.

The inputs for the deform function are:

   <ol>
       <li>**in_imgdef**: Deformation image. Has to be a .nii file.</li>
       <li>**indir**: Fiber input file.</li>
       <li>**outdir**: Result directory path.</li>
   </ol>

◆ inter2bundles()

def phybers.utils.utilities.inter2bundles (   dir_fib1,
  dir_fib2,
  outdir,
  d_th 
)

Calculates a similarity measure between two sets of brain fibers (fiber clusters or segmented bundles).

The inputs for the intersection function are:

  1. dir_fib1: First bundle file.
  2. dir_fib2: Second bundle file.
  3. outdir: Result directory path.
  4. d_th: TH_Dmax

◆ postprocessing()

def phybers.utils.utilities.postprocessing (   in_directory)

Contains a set of algorithms that are applied on the results of clustering and segmentation algorithms.

1) Fibers Lens (se calcula para el centroide del clúster) 2) Fibers Size ( cantidad de fibras por clúster) 3) Distancia intra-clúster mínima, Distancia intra promedio y Distancia intra máxima 4) Rij 5) DBindex

  1. in_directory: Flies directory path.

◆ sampling()

def phybers.utils.utilities.sampling (   indir,
  in_npoints,
  outdir 
)

Fiber sampling at n equidistant points.

The inputs for the sampling function are:

  1. indir: Fiber input file
  2. in_npoints: Number of points
  3. outdir: Result directory path.