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Add FSFAST parameter source to ArtifactDetect #706

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Oct 30, 2013
Merged

Add FSFAST parameter source to ArtifactDetect #706

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11 changes: 7 additions & 4 deletions nipype/algorithms/rapidart.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,18 +42,21 @@ def _get_affine_matrix(params, source):

params : np.array (upto 12 long) in native package format
source : the package that generated the parameters
supports SPM, AFNI, FSL, NIPY
supports SPM, AFNI, FSFAST, FSL, NIPY
"""
if source == 'FSL':
params = params[[3, 4, 5, 0, 1, 2]]
elif source == 'AFNI':
params = params[[4, 5, 3, 1, 2, 0]]
params[3:] = params[3:] * np.pi / 180.
elif source == 'FSFAST':
params = params[[5, 6, 4, 2, 3, 1]]
params[3:] = params[3:] * np.pi / 180.
if source == 'NIPY':
# nipy does not store typical euler angles, use nipy to convert
from nipy.algorithms.registration import to_matrix44
return to_matrix44(params)
#process for FSL, SPM and AFNI
#process for FSL, SPM, AFNI and FSFAST
rotfunc = lambda x: np.array([[np.cos(x), np.sin(x)],
[-np.sin(x), np.cos(x)]])
q = np.array([0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0])
Expand All @@ -76,7 +79,7 @@ def _get_affine_matrix(params, source):
# Shear
Sh = np.eye(4)
Sh[(0, 0, 1), (1, 2, 2)] = params[9:12]
if source == 'AFNI':
if source in ('AFNI', 'FSFAST'):
return np.dot(T, np.dot(Ry, np.dot(Rx, np.dot(Rz, np.dot(S, Sh)))))
return np.dot(T, np.dot(Rx, np.dot(Ry, np.dot(Rz, np.dot(S, Sh)))))

Expand Down Expand Up @@ -158,7 +161,7 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
realignment_parameters = InputMultiPath(File(exists=True), mandatory=True,
desc=("Names of realignment parameters"
"corresponding to the functional data files"))
parameter_source = traits.Enum("SPM", "FSL", "AFNI", "NiPy",
parameter_source = traits.Enum("SPM", "FSL", "AFNI", "NiPy", "FSFAST",
desc="Source of movement parameters",
mandatory=True)
use_differences = traits.ListBool([True, False], minlen=2, maxlen=2,
Expand Down