Skip to content
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

Jump to bottom

FIX caching of afni allineate when out_matrix is specified #3141

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
Open

FIX caching of afni allineate when out_matrix is specified #3141

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
7ef923a
generate out_matrix name
salma1601 Jan 4, 2020
2a1d705
update Allineate test
salma1601 Jan 4, 2020
7961a54
fix doctest
salma1601 Jan 5, 2020
5d68df6
split long line
salma1601 Jan 5, 2020
6c283dc
Merge remote-tracking branch 'upstream/master' into afni_allineate_ou…
effigies Feb 24, 2020
85aeffc
TEST: make specs
effigies Feb 24, 2020
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
6 changes: 5 additions & 1 deletion nipype/interfaces/afni/preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -283,6 +283,9 @@ class AllineateInputSpec(AFNICommandInputSpec):
)
out_matrix = File(
argstr="-1Dmatrix_save %s",
name_template='%s_allineated.aff12.1D',
name_source='in_file',
keep_extension=False,
desc="Save the transformation matrix for each volume.",
xor=["in_matrix", "allcostx"],
)
Expand Down Expand Up @@ -576,7 +579,8 @@ class Allineate(AFNICommand):
>>> allineate.inputs.reference = 'structural.nii'
>>> allineate.inputs.nwarp_fixmot = ['X', 'Y']
>>> allineate.cmdline
'3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii'
'3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate \
-1Dmatrix_save functional_allineated.aff12 -base structural.nii'
>>> res = allineate.run() # doctest: +SKIP
"""

Expand Down
7 changes: 6 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Allineate.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,12 @@ def test_Allineate_inputs():
xor=["allcostx"],
),
out_matrix=dict(
argstr="-1Dmatrix_save %s", extensions=None, xor=["in_matrix", "allcostx"],
argstr="-1Dmatrix_save %s",
extensions=None,
keep_extension=False,
name_source="in_file",
name_template="%s_allineated.aff12.1D",
xor=["in_matrix", "allcostx"],
),
out_param_file=dict(
argstr="-1Dparam_save %s",
Expand Down