interfaces.nipy.preprocess

ComputeMask

Link to code

Inputs:

[Mandatory]
mean_volume: (an existing file name)
        mean EPI image, used to compute the threshold for the mask

[Optional]
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: (an existing file name)
        reference volume used to compute the mask. If none is give, the mean
        volume is used.

Outputs:

brain_mask: (an existing file name)

SpaceTimeRealigner

Link to code

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.

Inputs:

[Mandatory]
in_file: (a list of items which are an existing file name)
        File to realign

[Optional]
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: 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: slice_times

Outputs:

out_file: (a list of items which are an existing file name)
        Realigned files
par_file: (a list of items which are an existing file name)
        Motion parameter files. Angles are not euler angles

Trim

Link to code

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() 

Inputs:

[Mandatory]
in_file: (an existing file name)
        EPI image to trim

[Optional]
begin_index: (an integer (int or long), nipype default value: 0)
        first volume
end_index: (an integer (int or long), nipype default value: 0)
        last volume indexed as in python (and 0 for last)
out_file: (a file name)
        output filename
suffix: (a unicode string, nipype default value: _trim)
        suffix for out_file to use if no out_file provided

Outputs:

out_file: (an existing file name)