Skip to content

[ENH] Enable cnr_maps and residuals outputs for FSL eddy #2750

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

Merged
merged 4 commits into from
Dec 10, 2018
Merged

[ENH] Enable cnr_maps and residuals outputs for FSL eddy #2750

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
a5b5aab
Add new parameters 'cnr_maps' and 'residuals' to FSL eddy interface
niklasfoe Oct 24, 2018
a8b157d
Merge branch 'master' into eddy
niklasfoe Nov 28, 2018
91ba894
Add min_ver flag to the new eddy input-traits
niklasfoe Dec 10, 2018
66ea26f
Merge branch 'master' into eddy
niklasfoe Dec 10, 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
18 changes: 18 additions & 0 deletions nipype/interfaces/fsl/epi.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -659,6 +659,10 @@ class EddyInputSpec(FSLCommandInputSpec):
"the field specified by --field and first volume "
"in file --imain")
use_cuda = traits.Bool(False, desc="Run eddy using cuda gpu")
cnr_maps = traits.Bool(
False, desc='Output CNR-Maps', argstr='--cnr_maps', min_ver='5.0.10')
residuals = traits.Bool(
False, desc='Output Residuals', argstr='--residuals', min_ver='5.0.10')


class EddyOutputSpec(TraitedSpec):
Expand All @@ -685,6 +689,10 @@ class EddyOutputSpec(TraitedSpec):
exists=True,
desc=('Text-file with a plain language report on what '
'outlier slices eddy has found'))
out_cnr_maps = File(
exists=True, desc='path/name of file with the cnr_maps')
out_residuals = File(
exists=True, desc='path/name of file with the residuals')


class Eddy(FSLCommand):
Expand Down Expand Up @@ -787,6 +795,16 @@ def _list_outputs(self):
self.inputs.out_base)
out_outlier_report = os.path.abspath(
'%s.eddy_outlier_report' % self.inputs.out_base)
if isdefined(self.inputs.cnr_maps) and self.inputs.cnr_maps:
out_cnr_maps = os.path.abspath(
'%s.eddy_cnr_maps.nii.gz' % self.inputs.out_base)
if os.path.exists(out_cnr_maps):
outputs['out_cnr_maps'] = out_cnr_maps
if isdefined(self.inputs.residuals) and self.inputs.residuals:
out_residuals = os.path.abspath(
'%s.eddy_residuals.nii.gz' % self.inputs.out_base)
if os.path.exists(out_residuals):
outputs['out_residuals'] = out_residuals

if os.path.exists(out_rotated_bvecs):
outputs['out_rotated_bvecs'] = out_rotated_bvecs
Expand Down
4 changes: 4 additions & 0 deletions nipype/interfaces/fsl/tests/test_auto_Eddy.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,8 @@ def test_Eddy_inputs():
session=dict(argstr='--session=%s', ),
slm=dict(argstr='--slm=%s', ),
use_cuda=dict(),
cnr_maps=dict(argstr='--cnr_maps', min_ver='5.0.10', ),
residuals=dict(argstr='--residuals', min_ver='5.0.10', ),
)
inputs = Eddy.input_spec()

Expand All @@ -89,6 +91,8 @@ def test_Eddy_outputs():
out_restricted_movement_rms=dict(),
out_rotated_bvecs=dict(),
out_shell_alignment_parameters=dict(),
out_cnr_maps=dict(),
out_residuals=dict(),
)
outputs = Eddy.output_spec()

Expand Down