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# 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
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    m: (a float)
            lower fraction of the histogram to be discarded
    mean_volume: (an existing file name)
            mean EPI image, used to compute the threshold for the mask
    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)

## FmriRealign4d

Link to code

Simultaneous motion and slice timing correction algorithm

This interface wraps nipy’s FmriRealign4d algorithm [1]_.

### Examples

    >>> from nipype.interfaces.nipy.preprocess import FmriRealign4d
    >>> realigner = FmriRealign4d()
    >>> realigner.inputs.in_file = ['functional.nii']
    >>> realigner.inputs.tr = 2
    >>> realigner.inputs.slice_order = range(0,67)
    >>> res = realigner.run()

### References

[1] | 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: (an existing file name)
            File to realign
    tr: (a float)
            TR in seconds

    [Optional]
    between_loops: (an integer, nipype default value: [5])
            loops used to realign different runs
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            File to realign
    loops: (an integer, nipype default value: [5])
            loops within each run
    slice_order: (a list of items which are an integer)
            0 based slice order. This would be equivalent to
            enteringnp.argsort(spm_slice_order) for this field. This
            effectsinterleaved acquisition. This field will be deprecated
            infuture Nipy releases and be replaced by actual sliceacquisition
            times.
            requires: time_interp
    speedup: (an integer, nipype default value: [5])
            successive image sub-sampling factors for acceleration
    start: (a float, nipype default value: 0.0)
            time offset into TR to align slices to
    time_interp: (True)
            Assume smooth changes across time e.g., fmri series. If you don't
            want slice timing correction set this to undefined
            requires: slice_order
    tr: (a float)
            TR in seconds
    tr_slices: (a float)
            TR slices
            requires: time_interp

Outputs:

    out_file: (an existing file name)
            Realigned files
    par_file: (an existing file name)
            Motion parameter files

## 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 [1]_ 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 = range(0, 3, 67)
    >>> realigner.inputs.slice_info = 2
    >>> res = realigner.run()

### References

[1] | 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: (an existing file name)
            File to realign

    [Optional]
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            File to realign
    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: 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: (an existing file name)
            Realigned files
    par_file: (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, nipype default value: 0)
            first volume
    end_index: (an integer, nipype default value: 0)
            last volume indexed as in python (and 0 for last)
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    in_file: (an existing file name)
            EPI image to trim
    out_file: (a file name)
            output filename
    suffix: (a string, nipype default value: _trim)
            suffix for out_file to use if no out_file provided

Outputs:

    out_file: (an existing file name)