nipype.interfaces.nipy.preprocess module

ComputeMask

Link to code

Bases: NipyBaseInterface

Mandatory Inputs:

mean_volume (a pathlike object or string representing an existing file) – Mean EPI image, used to compute the threshold for the mask.

Optional Inputs:

  • M (a float) – Upper fraction of the histogram to be discarded.

  • cc (a boolean) – Keep only the largest connected component.

  • m (a float) – Lower fraction of the histogram to be discarded.

  • reference_volume (a pathlike object or string representing an existing file) – Reference volume used to compute the mask. If none is give, the mean volume is used.

Outputs:

brain_mask (a pathlike object or string representing an existing file)

SpaceTimeRealigner

Link to code

Bases: NipyBaseInterface

Simultaneous motion and slice timing correction algorithm

If slice_times is not specified, this algorithm performs spatial motion correction

This interface wraps nipy’s SpaceTimeRealign algorithm [Roche2011] or simply the SpatialRealign algorithm when timing info is not provided.

Examples

>>> from nipype.interfaces.nipy import SpaceTimeRealigner
>>> #Run spatial realignment only
>>> realigner = SpaceTimeRealigner()
>>> realigner.inputs.in_file = ['functional.nii']
>>> res = realigner.run() 

>>> realigner = SpaceTimeRealigner()
>>> realigner.inputs.in_file = ['functional.nii']
>>> realigner.inputs.tr = 2
>>> realigner.inputs.slice_times = list(range(0, 3, 67))
>>> realigner.inputs.slice_info = 2
>>> res = realigner.run()

References

[Roche2011]

Roche A. A four-dimensional registration algorithm with application to joint correction of motion and slice timing in fMRI. IEEE Trans Med Imaging. 2011 Aug;30(8):1546-54. DOI.

Mandatory Inputs:

in_file (a list of items which are a pathlike object or string representing an existing file) – File to realign.

Optional Inputs:

  • slice_info (an integer or a list of items which are any value) – Single integer or length 2 sequence If int, the axis in images that is the slice axis. In a 4D image, this will often be axis = 2. If a 2 sequence, then elements are (slice_axis, slice_direction), where slice_axis is the slice axis in the image as above, and slice_direction is 1 if the slices were acquired slice 0 first, slice -1 last, or -1 if acquired slice -1 first, slice 0 last. If slice_info is an int, assume slice_direction == 1. Requires inputs: slice_times.

  • slice_times (a list of items which are a float or ‘asc_alt_2’ or ‘asc_alt_2_1’ or ‘asc_alt_half’ or ‘asc_alt_siemens’ or ‘ascending’ or ‘desc_alt_2’ or ‘desc_alt_half’ or ‘descending’) – Actual slice acquisition times.

  • tr (a float) – TR in seconds. Requires inputs: slice_times.

Outputs:

  • out_file (a list of items which are a pathlike object or string representing an existing file) – Realigned files.

  • par_file (a list of items which are a pathlike object or string representing an existing file) – Motion parameter files. Angles are not euler angles.

SpaceTimeRealigner.keywords = ['slice timing', 'motion correction']

Trim

Link to code

Bases: NipyBaseInterface

Simple interface to trim a few volumes from a 4d fmri nifti file

Examples

>>> from nipype.interfaces.nipy.preprocess import Trim
>>> trim = Trim()
>>> trim.inputs.in_file = 'functional.nii'
>>> trim.inputs.begin_index = 3 # remove 3 first volumes
>>> res = trim.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – EPI image to trim.

Optional Inputs:

  • begin_index (an integer) – First volume. (Nipype default value: 0)

  • end_index (an integer) – Last volume indexed as in python (and 0 for last). (Nipype default value: 0)

  • out_file (a pathlike object or string representing a file) – Output filename.

  • suffix (a string) – Suffix for out_file to use if no out_file provided. (Nipype default value: _trim)

Outputs:

out_file (a pathlike object or string representing an existing file)