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
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 = list(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: (a list of items which are an existing file name)
        File to realign
tr: (a float)
        TR in seconds

[Optional]
between_loops: (a list of items which are an integer (int or long),
         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
loops: (a list of items which are an integer (int or long), nipype
         default value: [5])
        loops within each run
slice_order: (a list of items which are an integer (int or long))
        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: (a list of items which are an integer (int or long), 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_slices: (a float)
        TR slices
        requires: time_interp

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

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]
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
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 u'asc_alt_2' or
         u'asc_alt_2_1' or u'asc_alt_half' or u'asc_alt_siemens' or
         u'ascending' or u'desc_alt_2' or u'desc_alt_half' or u'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)
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
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)