nipype.interfaces.nipy.preprocess module

ComputeMask

Link to code

Bases: NipyBaseInterface

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

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() # doctest: +SKIP

>>> 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() # doctest: +SKIP

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.
in_file : a list of items which are a pathlike object or string representing an existing file
File to realign.
slice_info : an integer (int or long) 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.
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() # doctest: +SKIP
in_file : a pathlike object or string representing an existing file
EPI image to trim.
begin_index : an integer (int or long)
First volume. (Nipype default value: 0)
end_index : an integer (int or long)
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 unicode string
Suffix for out_file to use if no out_file provided. (Nipype default value: _trim)

out_file : a pathlike object or string representing an existing file