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Commit 6b81d26

Browse files
author
Zach Lindsey
committed
Merge branch 'master' of https://github.com/zachlindsey/nipype 
2 parents 0953e5b + edf7a4a commit 6b81d26

23 files changed

+555
-54
lines changed

‎.github/workflows/contrib.yml

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -31,10 +31,10 @@ jobs:
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runs-on: ${{ matrix.os }}
3232
strategy:
3333
matrix:
34-
os: ['ubuntu-latest']
34+
os: ["ubuntu-latest"]
3535
python-version: [3.8]
36-
nipype-extras: ['dev']
37-
check: ['specs', 'style']
36+
nipype-extras: ["dev"]
37+
check: ["specs", "style"]
3838
env:
3939
DEPENDS: ""
4040
CHECK_TYPE: ${{ matrix.check }}

‎.github/workflows/tests.yml

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ on:
1919
- maint/*
2020
schedule:
2121
# 8am EST / 9am EDT Mondays
22-
- cron: '0 13 * * 1'
22+
- cron: "0 13 * * 1"
2323

2424
defaults:
2525
run:
@@ -57,7 +57,7 @@ jobs:
5757
needs: [build]
5858
strategy:
5959
matrix:
60-
package: ['wheel', 'sdist']
60+
package: ["wheel", "sdist"]
6161
steps:
6262
- uses: actions/download-artifact@v4
6363
with:
@@ -90,28 +90,28 @@ jobs:
9090
runs-on: ${{ matrix.os }}
9191
strategy:
9292
matrix:
93-
os: ['ubuntu-22.04']
94-
python-version: ['3.8', '3.9', '3.10', '3.11']
95-
check: ['test']
96-
pip-flags: ['']
97-
depends: ['REQUIREMENTS']
93+
os: ["ubuntu-22.04"]
94+
python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
95+
check: ["test"]
96+
pip-flags: [""]
97+
depends: ["REQUIREMENTS"]
9898
deb-depends: [false]
99-
nipype-extras: ['doc,tests,profiler']
99+
nipype-extras: ["doc,tests,profiler"]
100100
include:
101101
- os: ubuntu-22.04
102-
python-version: '3.8'
102+
python-version: "3.8"
103103
check: test
104-
pip-flags: ''
104+
pip-flags: ""
105105
depends: REQUIREMENTS
106106
deb-depends: true
107107
nipype-extras: doc,tests,profiler,duecredit,ssh
108-
#- os: ubuntu-20.04
109-
# python-version: 3.8
110-
# check: test
111-
#pip-flags: ''
112-
#depends: NUMPY123
113-
# deb-depends: true
114-
# nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
108+
- os: ubuntu-20.04
109+
python-version: 3.8
110+
check: test
111+
pip-flags: ""
112+
depends: REQUIREMENTS
113+
deb-depends: true
114+
nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
115115
env:
116116
DEPENDS: ${{ matrix.depends }}
117117
CHECK_TYPE: ${{ matrix.check }}

‎.github/workflows/tutorials.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@ name: Test tutorials
33
on:
44
push:
55
branches:
6-
- 'rel/*'
6+
- "rel/*"
77

88
concurrency:
99
group: tutorials-${{ github.ref }}

‎.zenodo.json

Lines changed: 16 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -891,16 +891,6 @@
891891
"name": "Mihai, Paul Glad",
892892
"orcid": "0000-0001-5715-6442"
893893
},
894-
{
895-
"affiliation": "Department of Psychology, Stanford University",
896-
"name": "Gorgolewski, Krzysztof J.",
897-
"orcid": "0000-0003-3321-7583"
898-
},
899-
{
900-
"affiliation": "MIT, HMS",
901-
"name": "Ghosh, Satrajit",
902-
"orcid": "0000-0002-5312-6729"
903-
},
904894
{
905895
"affiliation": "University of Tübingen and MPI for Biological Cybernertics",
906896
"name": "Bannert, Michael M.",
@@ -909,13 +899,27 @@
909899
{
910900
"affiliation": "Research Centre Juelich",
911901
"name": "Wu, Jianxiao",
912-
"orcid": "0000-0002-4866-272X",
902+
"orcid": "0000-0002-4866-272X"
903+
},
904+
{
905+
"affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany",
906+
"name": "Butry, Lionel"
913907
},
914908
{
915909
"affiliation": "Lund University",
916910
"name": "Anijärv, Toomas Erik",
917-
"orcid": "0000-0002-3650-4230",
911+
"orcid": "0000-0002-3650-4230"
912+
},
913+
{
914+
"affiliation": "Department of Psychology, Stanford University",
915+
"name": "Gorgolewski, Krzysztof J.",
916+
"orcid": "0000-0003-3321-7583"
918917
},
918+
{
919+
"affiliation": "MIT, HMS",
920+
"name": "Ghosh, Satrajit",
921+
"orcid": "0000-0002-5312-6729"
922+
}
919923
],
920924
"keywords": [
921925
"neuroimaging",

‎nipype/info.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -58,6 +58,7 @@ def get_nipype_gitversion():
5858
"Programming Language :: Python :: 3.9",
5959
"Programming Language :: Python :: 3.10",
6060
"Programming Language :: Python :: 3.11",
61+
"Programming Language :: Python :: 3.12",
6162
"Topic :: Scientific/Engineering",
6263
]
6364
PYTHON_REQUIRES = ">= 3.8"

‎nipype/interfaces/freesurfer/model.py

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -420,6 +420,14 @@ class GLMFitInputSpec(FSTraitedSpec):
420420
argstr="--logan %s %s %f",
421421
desc="RefTac TimeSec tstar : perform Logan kinetic modeling",
422422
)
423+
bp_clip_neg = traits.Bool(
424+
argstr="--bp-clip-neg",
425+
desc="set negative BP voxels to zero",
426+
)
427+
bp_clip_max = traits.Float(
428+
argstr="--bp-clip-max %f",
429+
desc="set BP voxels above max to max",
430+
)
423431
force_perm = traits.Bool(
424432
argstr="--perm-force",
425433
desc="force perumtation test, even when design matrix is not orthog",

‎nipype/interfaces/freesurfer/petsurfer.py

Lines changed: 34 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -458,10 +458,25 @@ class GTMPVCOutputSpec(TraitedSpec):
458458
yhat_with_noise = File(
459459
desc="4D PET file with full FOV of signal estimate (yhat) with noise after PVC (smoothed with PSF)",
460460
)
461+
eres = File(
462+
desc="4D PET file of residual error after PVC (smoothed with PSF)",
463+
)
464+
tissue_fraction = File(
465+
desc="4D PET file of tissue fraction before PVC",
466+
)
467+
tissue_fraction_psf = File(
468+
desc="4D PET file of tissue fraction after PVC (smoothed with PSF)",
469+
)
470+
seg = File(
471+
desc="Segmentation file of regions used for PVC",
472+
)
473+
seg_ctab = File(
474+
desc="Color table file for segmentation file",
475+
)
461476

462477

463478
class GTMPVC(FSCommand):
464-
"""create an anatomical segmentation for the geometric transfer matrix (GTM).
479+
"""Perform Partial Volume Correction (PVC) to PET Data.
465480
466481
Examples
467482
--------
@@ -536,6 +551,15 @@ def _list_outputs(self):
536551
outputs["gtm_stats"] = os.path.join(pvcdir, "gtm.stats.dat")
537552
outputs["reg_pet2anat"] = os.path.join(pvcdir, "aux", "bbpet2anat.lta")
538553
outputs["reg_anat2pet"] = os.path.join(pvcdir, "aux", "anat2bbpet.lta")
554+
outputs["eres"] = os.path.join(pvcdir, "eres.nii.gz")
555+
outputs["tissue_fraction"] = os.path.join(
556+
pvcdir, "aux", "tissue.fraction.nii.gz"
557+
)
558+
outputs["tissue_fraction_psf"] = os.path.join(
559+
pvcdir, "aux", "tissue.fraction.psf.nii.gz"
560+
)
561+
outputs["seg"] = os.path.join(pvcdir, "aux", "seg.nii.gz")
562+
outputs["seg_ctab"] = os.path.join(pvcdir, "aux", "seg.ctab")
539563

540564
# Assign the conditional outputs
541565
if self.inputs.save_input:
@@ -562,7 +586,7 @@ def _list_outputs(self):
562586
return outputs
563587

564588

565-
class MRTMInputSpec(GLMFitInputSpec):
589+
class MRTM1InputSpec(GLMFitInputSpec):
566590
mrtm1 = traits.Tuple(
567591
File(exists=True),
568592
File(exists=True),
@@ -572,20 +596,20 @@ class MRTMInputSpec(GLMFitInputSpec):
572596
)
573597

574598

575-
class MRTM(GLMFit):
599+
class MRTM1(GLMFit):
576600
"""Perform MRTM1 kinetic modeling.
577601
578602
Examples
579603
--------
580-
>>> mrtm = MRTM()
604+
>>> mrtm = MRTM1()
581605
>>> mrtm.inputs.in_file = 'tac.nii'
582606
>>> mrtm.inputs.mrtm1 = ('ref_tac.dat', 'timing.dat')
583607
>>> mrtm.inputs.glm_dir = 'mrtm'
584608
>>> mrtm.cmdline
585609
'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
586610
"""
587611

588-
input_spec = MRTMInputSpec
612+
input_spec = MRTM1InputSpec
589613

590614

591615
class MRTM2InputSpec(GLMFitInputSpec):
@@ -614,7 +638,7 @@ class MRTM2(GLMFit):
614638
input_spec = MRTM2InputSpec
615639

616640

617-
class LoganRefInputSpec(GLMFitInputSpec):
641+
class LoganInputSpec(GLMFitInputSpec):
618642
logan = traits.Tuple(
619643
File(exists=True),
620644
File(exists=True),
@@ -625,16 +649,16 @@ class LoganRefInputSpec(GLMFitInputSpec):
625649
)
626650

627651

628-
class LoganRef(GLMFit):
629-
"""Perform Logan reference kinetic modeling.
652+
class Logan(GLMFit):
653+
"""Perform Logan kinetic modeling.
630654
Examples
631655
--------
632-
>>> logan = LoganRef()
656+
>>> logan = Logan()
633657
>>> logan.inputs.in_file = 'tac.nii'
634658
>>> logan.inputs.logan = ('ref_tac.dat', 'timing.dat', 2600)
635659
>>> logan.inputs.glm_dir = 'logan'
636660
>>> logan.cmdline
637661
'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'
638662
"""
639663

640-
input_spec = LoganRefInputSpec
664+
input_spec = LoganInputSpec

‎nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,12 @@ def test_GLMFit_inputs():
1313
args=dict(
1414
argstr="%s",
1515
),
16+
bp_clip_max=dict(
17+
argstr="--bp-clip-max %f",
18+
),
19+
bp_clip_neg=dict(
20+
argstr="--bp-clip-neg",
21+
),
1622
calc_AR1=dict(
1723
argstr="--tar1",
1824
),

‎nipype/interfaces/freesurfer/tests/test_auto_GTMPVC.py

Lines changed: 15 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -207,6 +207,9 @@ def test_GTMPVC_inputs():
207207

208208
def test_GTMPVC_outputs():
209209
output_map = dict(
210+
eres=dict(
211+
extensions=None,
212+
),
210213
gtm_file=dict(
211214
extensions=None,
212215
),
@@ -256,6 +259,18 @@ def test_GTMPVC_outputs():
256259
reg_rbvpet2anat=dict(
257260
extensions=None,
258261
),
262+
seg=dict(
263+
extensions=None,
264+
),
265+
seg_ctab=dict(
266+
extensions=None,
267+
),
268+
tissue_fraction=dict(
269+
extensions=None,
270+
),
271+
tissue_fraction_psf=dict(
272+
extensions=None,
273+
),
259274
yhat=dict(
260275
extensions=None,
261276
),

‎nipype/interfaces/freesurfer/tests/test_auto_LoganRef.py renamed to ‎nipype/interfaces/freesurfer/tests/test_auto_Logan.py

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
2-
from ..petsurfer import LoganRef
2+
from ..petsurfer import Logan
33

44

5-
def test_LoganRef_inputs():
5+
def test_Logan_inputs():
66
input_map = dict(
77
allow_ill_cond=dict(
88
argstr="--illcond",
@@ -13,6 +13,12 @@ def test_LoganRef_inputs():
1313
args=dict(
1414
argstr="%s",
1515
),
16+
bp_clip_max=dict(
17+
argstr="--bp-clip-max %f",
18+
),
19+
bp_clip_neg=dict(
20+
argstr="--bp-clip-neg",
21+
),
1622
calc_AR1=dict(
1723
argstr="--tar1",
1824
),
@@ -214,14 +220,14 @@ def test_LoganRef_inputs():
214220
xor=("weight_file", "weight_inv", "weight_sqrt"),
215221
),
216222
)
217-
inputs = LoganRef.input_spec()
223+
inputs = Logan.input_spec()
218224

219225
for key, metadata in list(input_map.items()):
220226
for metakey, value in list(metadata.items()):
221227
assert getattr(inputs.traits()[key], metakey) == value
222228

223229

224-
def test_LoganRef_outputs():
230+
def test_Logan_outputs():
225231
output_map = dict(
226232
beta_file=dict(
227233
extensions=None,
@@ -271,7 +277,7 @@ def test_LoganRef_outputs():
271277
extensions=None,
272278
),
273279
)
274-
outputs = LoganRef.output_spec()
280+
outputs = Logan.output_spec()
275281

276282
for key, metadata in list(output_map.items()):
277283
for metakey, value in list(metadata.items()):

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