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Commit 1b5793a

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Merge pull request #3602 from mnoergaard/update_petsurfer
ENH: Update PETsurfer interface
2 parents d2f4953 + 6b7bda4 commit 1b5793a

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8 files changed

+97
-20
lines changed

8 files changed

+97
-20
lines changed

‎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()):

‎nipype/interfaces/freesurfer/tests/test_auto_MRTM.py‎ renamed to ‎nipype/interfaces/freesurfer/tests/test_auto_MRTM1.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 MRTM
2+
from ..petsurfer import MRTM1
33

44

5-
def test_MRTM_inputs():
5+
def test_MRTM1_inputs():
66
input_map = dict(
77
allow_ill_cond=dict(
88
argstr="--illcond",
@@ -13,6 +13,12 @@ def test_MRTM_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_MRTM_inputs():
214220
xor=("weight_file", "weight_inv", "weight_sqrt"),
215221
),
216222
)
217-
inputs = MRTM.input_spec()
223+
inputs = MRTM1.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_MRTM_outputs():
230+
def test_MRTM1_outputs():
225231
output_map = dict(
226232
beta_file=dict(
227233
extensions=None,
@@ -271,7 +277,7 @@ def test_MRTM_outputs():
271277
extensions=None,
272278
),
273279
)
274-
outputs = MRTM.output_spec()
280+
outputs = MRTM1.output_spec()
275281

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

‎nipype/interfaces/freesurfer/tests/test_auto_MRTM2.py‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,12 @@ def test_MRTM2_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_OneSampleTTest.py‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,12 @@ def test_OneSampleTTest_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
),

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