nipype.interfaces.nipy.preprocess module

ComputeMask

Link to code

Bases: NipyBaseInterface

mean_volumea pathlike object or string representing an existing file

Mean EPI image, used to compute the threshold for the mask.

Ma float

Upper fraction of the histogram to be discarded.

cca boolean

Keep only the largest connected component.

ma float

Lower fraction of the histogram to be discarded.

reference_volumea 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() 
>>> 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.

in_filea list of items which are a pathlike object or string representing an existing file

File to realign.

slice_infoan 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_timesa 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.

tra float

TR in seconds. Requires inputs: slice_times.

out_filea list of items which are a pathlike object or string representing an existing file

Realigned files.

par_filea 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() 
in_filea pathlike object or string representing an existing file

EPI image to trim.

begin_indexan integer (int or long)

First volume. (Nipype default value: 0)

end_indexan integer (int or long)

Last volume indexed as in python (and 0 for last). (Nipype default value: 0)

out_filea pathlike object or string representing a file

Output filename.

suffixa 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