niworkflows.interfaces.header module¶

Handling NIfTI headers.

class niworkflows.interfaces.header.CopyHeader(from_file=None, resource_monitor=None, **inputs)[source]¶

Bases: SimpleInterface

Copy a header from the hdr_file to out_file with data drawn from in_file.

Mandatory Inputs:

hdr_file (a pathlike object or string representing an existing file) – The file we get the header from.
in_file (a pathlike object or string representing an existing file) – The file we get the data from.

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.

class niworkflows.interfaces.header.CopyXForm(fields=None, **inputs)[source]¶

Bases: SimpleInterface

Copy the x-form orientation headers from hdr_file to an arbitrary set of images.

Target images that will get their x-form headers replaced should be prescribed using the fields argument at interface instantiation.

Mandatory Inputs:: hdr_file (a pathlike object or string representing an existing file) – The file we get the header from.

output_spec¶: alias of DynamicTraitedSpec

class niworkflows.interfaces.header.MatchHeader(from_file=None, resource_monitor=None, **inputs)[source]¶

Bases: SimpleInterface

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – NIfTI file which header will be checked.
reference (a pathlike object or string representing an existing file) – NIfTI file with reference header.

Outputs:

out_file (a pathlike object or string representing an existing file) – NIfTI file with fixed header.

class niworkflows.interfaces.header.SanitizeImage(from_file=None, resource_monitor=None, **inputs)[source]¶

Bases: SimpleInterface

Check the correctness of x-form headers (matrix and code) and fixes problematic combinations of values. Removes any extension form the header if present. This interface implements the following logic:

`SanitizeImage` truth table¶
valid quaternions	`qform_code` > 0	`sform_code` > 0	`qform == sform`	actions
`True`	`True`	`True`	`True`	None
`True`	`True`	`False`	*	sform, scode <- qform, qcode
*	`True`	*	`False`	sform, scode <- qform, qcode
*	`False`	`True`	*	qform, qcode <- sform, scode
*	`False`	`False`	*	sform, qform <- best affine; scode, qcode <- 1
`False`	*	`False`	*	sform, qform <- best affine; scode, qcode <- 1

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input image.

Optional Inputs:

max_32bit (a boolean) – Cast data to float32 if higher precision is encountered. (Nipype default value: False)
n_volumes_to_discard (an integer) – Discard n first volumes. (Nipype default value: 0)

Outputs:

out_file (a pathlike object or string representing an existing file) – Validated image.
out_report (a pathlike object or string representing an existing file) – HTML segment containing warning.

class niworkflows.interfaces.header.ValidateImage(from_file=None, resource_monitor=None, **inputs)[source]¶

Bases: SimpleInterface

Check the correctness of x-form headers (matrix and code).

This interface implements the following logic:

`ValidateImage` truth table¶
valid quaternions	`qform_code` > 0	`sform_code` > 0	`qform == sform`	actions
`True`	`True`	`True`	`True`	None
`True`	`True`	`False`	*	sform, scode <- qform, qcode
*	*	`True`	`False`	qform, qcode <- sform, scode
*	`False`	`True`	*	qform, qcode <- sform, scode
*	`False`	`False`	*	sform, qform <- best affine; scode, qcode <- 1
`False`	*	`False`	*	sform, qform <- best affine; scode, qcode <- 1

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input image.

Outputs:

out_file (a pathlike object or string representing an existing file) – Validated image.
out_report (a pathlike object or string representing an existing file) – HTML segment containing warning.