Merge branch 'master' of https://github.com/zachlindsey/nipype

Author: Zach Lindsey

.github/workflows/contrib.yml

@@ -31,10 +31,10 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-latest']
+        os: ["ubuntu-latest"]
         python-version: [3.8]
-        nipype-extras: ['dev']
-        check: ['specs', 'style']
+        nipype-extras: ["dev"]
+        check: ["specs", "style"]
     env:
       DEPENDS: ""
       CHECK_TYPE: ${{ matrix.check }}

.github/workflows/tests.yml

@@ -19,7 +19,7 @@ on:
       - maint/*
   schedule:
     # 8am EST / 9am EDT Mondays
-    - cron: '0 13 * * 1'
+    - cron: "0 13 * * 1"
 
 defaults:
   run:
@@ -57,7 +57,7 @@ jobs:
     needs: [build]
     strategy:
       matrix:
-        package: ['wheel', 'sdist']
+        package: ["wheel", "sdist"]
     steps:
       - uses: actions/download-artifact@v4
         with:
@@ -90,28 +90,28 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ['ubuntu-22.04']
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        check: ['test']
-        pip-flags: ['']
-        depends: ['REQUIREMENTS']
+        os: ["ubuntu-22.04"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        check: ["test"]
+        pip-flags: [""]
+        depends: ["REQUIREMENTS"]
         deb-depends: [false]
-        nipype-extras: ['doc,tests,profiler']
+        nipype-extras: ["doc,tests,profiler"]
         include:
           - os: ubuntu-22.04
-            python-version: '3.8'
+            python-version: "3.8"
             check: test
-            pip-flags: ''
+            pip-flags: ""
             depends: REQUIREMENTS
             deb-depends: true
             nipype-extras: doc,tests,profiler,duecredit,ssh
-          # - os: ubuntu-20.04
-          #   python-version: 3.8
-          #   check: test
-          #   pip-flags: ''
-          #   depends: NUMPY123
-          #   deb-depends: true
-          #   nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
+          - os: ubuntu-20.04
+            python-version: 3.8
+            check: test
+            pip-flags: ""
+            depends: REQUIREMENTS
+            deb-depends: true
+            nipype-extras: doc,tests,nipy,profiler,duecredit,ssh
     env:
       DEPENDS: ${{ matrix.depends }}
       CHECK_TYPE: ${{ matrix.check }}

.github/workflows/tutorials.yml

@@ -3,7 +3,7 @@ name: Test tutorials
 on:
   push:
     branches:
-      - 'rel/*'
+      - "rel/*"
 
 concurrency:
   group: tutorials-${{ github.ref }}

.zenodo.json

@@ -891,16 +891,6 @@
       "name": "Mihai, Paul Glad",
       "orcid": "0000-0001-5715-6442"
     },
-    {
-      "affiliation": "Department of Psychology, Stanford University",
-      "name": "Gorgolewski, Krzysztof J.",
-      "orcid": "0000-0003-3321-7583"
-    },
-    {
-      "affiliation": "MIT, HMS",
-      "name": "Ghosh, Satrajit",
-      "orcid": "0000-0002-5312-6729"
-    },
     {
       "affiliation": "University of Tübingen and MPI for Biological Cybernertics",
       "name": "Bannert, Michael M.",
@@ -909,13 +899,27 @@
     {
       "affiliation": "Research Centre Juelich",
       "name": "Wu, Jianxiao",
-      "orcid": "0000-0002-4866-272X",
+      "orcid": "0000-0002-4866-272X"
+    },
+    {
+      "affiliation": "Department of Neurology, BG-University Hospital Bergmannsheil Bochum, Germany",
+      "name": "Butry, Lionel"
     },
     {
       "affiliation": "Lund University",
       "name": "Anijärv, Toomas Erik",
-      "orcid": "0000-0002-3650-4230",
+      "orcid": "0000-0002-3650-4230"
+    },
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Gorgolewski, Krzysztof J.",
+      "orcid": "0000-0003-3321-7583"
     },
+    {
+      "affiliation": "MIT, HMS",
+      "name": "Ghosh, Satrajit",
+      "orcid": "0000-0002-5312-6729"
+    }
   ],
   "keywords": [
     "neuroimaging",

nipype/info.py

@@ -58,6 +58,7 @@ def get_nipype_gitversion():
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
 ]
 PYTHON_REQUIRES = ">= 3.8"

nipype/interfaces/freesurfer/model.py

@@ -420,6 +420,14 @@ class GLMFitInputSpec(FSTraitedSpec):
         argstr="--logan %s %s %f",
         desc="RefTac TimeSec tstar   : perform Logan kinetic modeling",
     )
+    bp_clip_neg = traits.Bool(
+        argstr="--bp-clip-neg",
+        desc="set negative BP voxels to zero",
+    )
+    bp_clip_max = traits.Float(
+        argstr="--bp-clip-max %f",
+        desc="set BP voxels above max to max",
+    )
     force_perm = traits.Bool(
         argstr="--perm-force",
         desc="force perumtation test, even when design matrix is not orthog",

nipype/interfaces/freesurfer/petsurfer.py

@@ -458,10 +458,25 @@ class GTMPVCOutputSpec(TraitedSpec):
     yhat_with_noise = File(
         desc="4D PET file with full FOV of signal estimate (yhat) with noise after PVC (smoothed with PSF)",
     )
+    eres = File(
+        desc="4D PET file of residual error after PVC (smoothed with PSF)",
+    )
+    tissue_fraction = File(
+        desc="4D PET file of tissue fraction before PVC",
+    )
+    tissue_fraction_psf = File(
+        desc="4D PET file of tissue fraction after PVC (smoothed with PSF)",
+    )
+    seg = File(
+        desc="Segmentation file of regions used for PVC",
+    )
+    seg_ctab = File(
+        desc="Color table file for segmentation file",
+    )
 
 
 class GTMPVC(FSCommand):
-    """create an anatomical segmentation for the geometric transfer matrix (GTM).
+    """Perform Partial Volume Correction (PVC) to PET Data.
 
     Examples
     --------
@@ -536,6 +551,15 @@ def _list_outputs(self):
         outputs["gtm_stats"] = os.path.join(pvcdir, "gtm.stats.dat")
         outputs["reg_pet2anat"] = os.path.join(pvcdir, "aux", "bbpet2anat.lta")
         outputs["reg_anat2pet"] = os.path.join(pvcdir, "aux", "anat2bbpet.lta")
+        outputs["eres"] = os.path.join(pvcdir, "eres.nii.gz")
+        outputs["tissue_fraction"] = os.path.join(
+            pvcdir, "aux", "tissue.fraction.nii.gz"
+        )
+        outputs["tissue_fraction_psf"] = os.path.join(
+            pvcdir, "aux", "tissue.fraction.psf.nii.gz"
+        )
+        outputs["seg"] = os.path.join(pvcdir, "aux", "seg.nii.gz")
+        outputs["seg_ctab"] = os.path.join(pvcdir, "aux", "seg.ctab")
 
         # Assign the conditional outputs
         if self.inputs.save_input:
@@ -562,7 +586,7 @@ def _list_outputs(self):
         return outputs
 
 
-class MRTMInputSpec(GLMFitInputSpec):
+class MRTM1InputSpec(GLMFitInputSpec):
     mrtm1 = traits.Tuple(
         File(exists=True),
         File(exists=True),
@@ -572,20 +596,20 @@ class MRTMInputSpec(GLMFitInputSpec):
     )
 
 
-class MRTM(GLMFit):
+class MRTM1(GLMFit):
     """Perform MRTM1 kinetic modeling.
 
     Examples
     --------
-    >>> mrtm = MRTM()
+    >>> mrtm = MRTM1()
     >>> mrtm.inputs.in_file = 'tac.nii'
     >>> mrtm.inputs.mrtm1 = ('ref_tac.dat', 'timing.dat')
     >>> mrtm.inputs.glm_dir = 'mrtm'
     >>> mrtm.cmdline
     'mri_glmfit --glmdir mrtm --y tac.nii --mrtm1 ref_tac.dat timing.dat'
     """
 
-    input_spec = MRTMInputSpec
+    input_spec = MRTM1InputSpec
 
 
 class MRTM2InputSpec(GLMFitInputSpec):
@@ -614,7 +638,7 @@ class MRTM2(GLMFit):
     input_spec = MRTM2InputSpec
 
 
-class LoganRefInputSpec(GLMFitInputSpec):
+class LoganInputSpec(GLMFitInputSpec):
     logan = traits.Tuple(
         File(exists=True),
         File(exists=True),
@@ -625,16 +649,16 @@ class LoganRefInputSpec(GLMFitInputSpec):
     )
 
 
-class LoganRef(GLMFit):
-    """Perform Logan reference kinetic modeling.
+class Logan(GLMFit):
+    """Perform Logan kinetic modeling.
     Examples
     --------
-    >>> logan = LoganRef()
+    >>> logan = Logan()
     >>> logan.inputs.in_file = 'tac.nii'
     >>> logan.inputs.logan = ('ref_tac.dat', 'timing.dat', 2600)
     >>> logan.inputs.glm_dir = 'logan'
     >>> logan.cmdline
     'mri_glmfit --glmdir logan --y tac.nii --logan ref_tac.dat timing.dat 2600'
     """
 
-    input_spec = LoganRefInputSpec
+    input_spec = LoganInputSpec

nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py

@@ -13,6 +13,12 @@ def test_GLMFit_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),

nipype/interfaces/freesurfer/tests/test_auto_GTMPVC.py

@@ -207,6 +207,9 @@ def test_GTMPVC_inputs():
 
 def test_GTMPVC_outputs():
     output_map = dict(
+        eres=dict(
+            extensions=None,
+        ),
         gtm_file=dict(
             extensions=None,
         ),
@@ -256,6 +259,18 @@ def test_GTMPVC_outputs():
         reg_rbvpet2anat=dict(
             extensions=None,
         ),
+        seg=dict(
+            extensions=None,
+        ),
+        seg_ctab=dict(
+            extensions=None,
+        ),
+        tissue_fraction=dict(
+            extensions=None,
+        ),
+        tissue_fraction_psf=dict(
+            extensions=None,
+        ),
         yhat=dict(
             extensions=None,
         ),

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

@@ -1,8 +1,8 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from ..petsurfer import LoganRef
+from ..petsurfer import Logan
 
 
-def test_LoganRef_inputs():
+def test_Logan_inputs():
     input_map = dict(
         allow_ill_cond=dict(
             argstr="--illcond",
@@ -13,6 +13,12 @@ def test_LoganRef_inputs():
         args=dict(
             argstr="%s",
         ),
+        bp_clip_max=dict(
+            argstr="--bp-clip-max %f",
+        ),
+        bp_clip_neg=dict(
+            argstr="--bp-clip-neg",
+        ),
         calc_AR1=dict(
             argstr="--tar1",
         ),
@@ -214,14 +220,14 @@ def test_LoganRef_inputs():
             xor=("weight_file", "weight_inv", "weight_sqrt"),
         ),
     )
-    inputs = LoganRef.input_spec()
+    inputs = Logan.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 
 
-def test_LoganRef_outputs():
+def test_Logan_outputs():
     output_map = dict(
         beta_file=dict(
             extensions=None,
@@ -271,7 +277,7 @@ def test_LoganRef_outputs():
             extensions=None,
         ),
     )
-    outputs = LoganRef.output_spec()
+    outputs = Logan.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):