Skip to content

[WIP][FIX] Bug ApplyInverseTransform #3326

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 5 commits into from
Closed

[WIP][FIX] Bug ApplyInverseTransform #3326

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
d9bda43
coorected field -> out{1}.pull for in_files and interpolation
davidmeunier79 Apr 14, 2021
6510863
modified the formating of inputs (reference has to be one image for s…
davidmeunier79 Apr 14, 2021
93c1d6b
Merge remote-tracking branch 'upstream/master' into bug_apply_inv
effigies Apr 30, 2021
ab42259
STY: black
effigies Apr 30, 2021
527699c
TEST: make specs
effigies Apr 30, 2021
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
4 changes: 2 additions & 2 deletions nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,11 @@ def test_ApplyInverseDeformation_inputs():
xor=["deformation"],
),
in_files=dict(
field="fnames",
field="out{1}.pull.fnames",
mandatory=True,
),
interpolation=dict(
field="interp",
field="out{1}.pull.interp",
),
matlab_cmd=dict(),
mfile=dict(
Expand Down
14 changes: 10 additions & 4 deletions nipype/interfaces/spm/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -262,12 +262,13 @@ class ApplyInverseDeformationInput(SPMCommandInputSpec):
in_files = InputMultiPath(
File(exists=True),
mandatory=True,
field="fnames",
field="out{1}.pull.fnames",
desc="Files on which deformation is applied",
)
target = File(
exists=True, field="comp{1}.inv.space", desc="File defining target space"
)

deformation = File(
exists=True,
field="comp{1}.inv.comp{1}.sn2def.matname",
Expand All @@ -281,7 +282,10 @@ class ApplyInverseDeformationInput(SPMCommandInputSpec):
xor=["deformation"],
)
interpolation = traits.Range(
low=0, high=7, field="interp", desc="degree of b-spline used for interpolation"
low=0,
high=7,
field="out{1}.pull.interp",
desc="degree of b-spline used for interpolation",
)

bounding_box = traits.List(
Expand Down Expand Up @@ -328,9 +332,11 @@ class ApplyInverseDeformation(SPMCommand):
def _format_arg(self, opt, spec, val):
"""Convert input to appropriate format for spm"""
if opt == "in_files":
return scans_for_fnames(ensure_list(val))
return np.array([simplify_list(val)], dtype=object)
# return scans_for_fnames(ensure_list(val))
if opt == "target":
return scans_for_fname(ensure_list(val))
return np.array([simplify_list(val)], dtype=object)
# return scans_for_fname(ensure_list(val))
if opt == "deformation":
return np.array([simplify_list(val)], dtype=object)
if opt == "deformation_field":
Expand Down