Skip to content

[WIP] ENH: Read 4dfp_tools motion parameters #2765

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
wants to merge 2 commits into from
Closed

[WIP] ENH: Read 4dfp_tools motion parameters #2765

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
48ec226
ENH: Read 4dfp_tools motion parameters
effigies Oct 29, 2018
a02433c
Merge remote-tracking branch 'upstream/master' into enh/4dfp_motion_p…
effigies Dec 17, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions nipype/algorithms/confounds.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -233,6 +233,7 @@ class FramewiseDisplacementInputSpec(BaseInterfaceInputSpec):
"SPM",
"FSFAST",
"NIPY",
"4DFP",
desc="Source of movement parameters",
mandatory=True)
radius = traits.Float(
Expand Down
1 change: 1 addition & 0 deletions nipype/algorithms/modelgen.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ class SpecifyModelInputSpec(BaseInterfaceInputSpec):
"AFNI",
"FSFAST",
"NIPY",
"4DFP",
usedefault=True,
desc="Source of motion parameters")
outlier_files = InputMultiPath(
Expand Down
3 changes: 2 additions & 1 deletion nipype/algorithms/rapidart.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ 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, FSFAST, FSL, NIPY
supports SPM, AFNI, FSFAST, FSL, NIPY, 4DFP
"""
if source == 'NIPY':
# nipy does not store typical euler angles, use nipy to convert
Expand Down Expand Up @@ -173,6 +173,7 @@ class ArtifactDetectInputSpec(BaseInterfaceInputSpec):
"AFNI",
"NiPy",
"FSFAST",
"4DFP",
desc="Source of movement parameters",
mandatory=True)
use_differences = traits.ListBool(
Expand Down
3 changes: 3 additions & 0 deletions nipype/utils/misc.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -283,6 +283,9 @@ def normalize_mc_params(params, source):
elif source.upper() in ('AFNI', 'FSFAST'):
params = params[np.asarray([4, 5, 3, 1, 2, 0]) + (len(params) > 6)]
params[3:] = params[3:] * np.pi / 180.
elif source.upper() == '4DFP':
params = params[np.arange(1, 7)]
params[3:] = params[3:] * np.pi / 180.
elif source.upper() == 'NIPY':
from nipy.algorithms.registration import to_matrix44, aff2euler
matrix = to_matrix44(params)
Expand Down