Utilities for extracting information on various input files using MRtrix3’s mrinfo tool. All values are returned in basic Python data types.
- designer.preprocessing.mrinfoutil.commandhistory(path)¶
Returns a list of command history (manipulations or transformations) performed on MRtrix file format .mif
- Parameters
path (str) – Path to input image or directory
- Returns
command history of input file
- Return type
list of str
- designer.preprocessing.mrinfoutil.datatype(path)¶
Returns the data type used for storing input DWI
- Parameters
path (str) – Path to input image or directory
- Returns
MRtrix3 datatype
- Return type
str
- designer.preprocessing.mrinfoutil.dwscheme(path)¶
Returns a list of input DWI’s diffusion weighting scheme
- Parameters
path (str) – Path to input image or directory
- Returns
diffusion weighing scheme
- Return type
list of float
- designer.preprocessing.mrinfoutil.echotime(path)¶
Returns the echo time(s) of DWI in miliseconds
- Parameters
path (str) – Path to input image or directory
- Returns
int if all DWIs have the same echo time – Echo time in miliseconds
str if all DWIs have different echo time – ‘variable’
- designer.preprocessing.mrinfoutil.format(path)¶
Returns the file format of input DWI
- Parameters
path (str) – Path to input image or directory
- Returns
Image file format
- Return type
str
- designer.preprocessing.mrinfoutil.getconsole(path, flag)¶
Fetches the console output of MRtrix3’s mrinfo with specified flag
- Parameters
path (str) – Path to input image or directory
flag (str) – Flag to pass onto mrinfo
- Returns
MRtrix3’s mrinfo console output
- Return type
str
- designer.preprocessing.mrinfoutil.is_fullsphere(path)¶
Returns boolean value indicating whether input file has full spherical sampling
- Parameters
path (str) – Path to input image or directory
- Returns
True if full spherical sampling False if half-spherical sampling
- Return type
bool
- designer.preprocessing.mrinfoutil.max_shell(path)¶
Returns the maximum b-value shell in DWI
- Parameters
path (str) – Path to input image or directory
- Returns
Max b-value
- Return type
int
- designer.preprocessing.mrinfoutil.multiplier(path)¶
Returns the input DWI’s intensity multiplier
- Parameters
path (str) – Path to input image or directory
- Returns
Image intensity multiplier
- Return type
float
- designer.preprocessing.mrinfoutil.ndim(path)¶
Returns the number of image dimensions of input DWI
- Parameters
path (str) – Path to input image or directory
- Returns
Number of dimensions in image
- Return type
int
- designer.preprocessing.mrinfoutil.num_shells(path)¶
Returns the number of b-value shells detected in input file
- Parameters
path (str) – Path to input image or directory
- Returns
Number of shells
- Return type
int
- designer.preprocessing.mrinfoutil.offset(path)¶
Returns the input DWI’s intensity offset
- Parameters
path (str) – Path to input image or directory
- Returns
Image intensity offset
- Return type
float
- designer.preprocessing.mrinfoutil.pescheme(path)¶
Returns a list of phase encoding scheme. If len(pescheme) > 1, the .mif DWI contains more than one directons
- Parameters
path (str) – Path to input image or directory
- Returns
nPE (int) – Number of PE directions
PE (int or list of int) – Phase encoding direction(s)
- designer.preprocessing.mrinfoutil.shells(path)¶
Returns the number of b-value shells detected in input file
- Parameters
path (str) – Path to input image or directory
- Returns
Number of shells
- Return type
int
- designer.preprocessing.mrinfoutil.size(path)¶
Returns the size of input DWI image along each axis
- Parameters
path (str) – Path to input image or directory
- Returns
Number of voxels in [X, Y, Z, B-value]
- Return type
tuple of int
- designer.preprocessing.mrinfoutil.spacing(path)¶
Returns the voxel spacing along each of input DWI’s dimensions
- Parameters
path (str) – Path to input image or directory
- Returns
Number of spacing between voxels [X, Y, Z, B-value]
- Return type
tuple of int
- designer.preprocessing.mrinfoutil.strides(path)¶
Returns data strides of input DWI
- Parameters
path (str) – Path to input image or directory
- Returns
MRtrix3’s strides
- Return type
tuple of ints
- designer.preprocessing.mrinfoutil.transform(path)¶
Returns the input DWI’s 4x4 voxel to image transformation matrix
- Parameters
path (str) – Path to input image or directory
- Returns
Image transformation matrix
- Return type
tuple of float