nipype.interfaces.nipy.preprocess module¶
ComputeMask¶
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¶
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 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)
, whereslice_axis
is the slice axis in the image as above, andslice_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, assumeslice_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¶
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
First volume. (Nipype default value:
0
)- end_indexan integer
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 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