Merge branch 'master' into dwifslpreproc

Author: GalKepler

.github/workflows/package.yml

@@ -8,6 +8,9 @@ on:
       - rel/*
     tags:
       - '*'
+  schedule:
+    # 8am EST / 9am EDT Mondays
+    - cron: '0 13 * * 1'
 
 defaults:
   run:

.github/workflows/tests.yml

@@ -15,6 +15,9 @@ on:
     branches:
       - master
       - maint/*
+  schedule:
+    # 8am EST / 9am EDT Mondays
+    - cron: '0 13 * * 1'
 
 defaults:
   run:

.mailmap

@@ -75,7 +75,10 @@ Franz Liem <franz.liem@gmail.com>
 Franz Liem <franz.liem@gmail.com> <franz.liem>
 Fred Loney <loneyf@ohsu.edu>
 Gael Varoquaux <gael.varoquaux@normalesup.org>
+Gal Ben-Zvi <hershkovitz1@mail.tau.ac.il>
 Gavin Cooper <Gavin.Cooper@newcastle.edu.au> <gjcooper@gmail.com>
+Ghislain Vaillant <ghislain.vaillant@icm-institute.org>
+Ghislain Vaillant <ghislain.vaillant@icm-institute.org> <ghisvail@users.noreply.github.com>
 Gilles de Hollander <gilles.de.hollander@gmail.com>
 Gio Piantoni <github@gpiantoni.com>
 Guillaume Flandin <guillaume.flandin@gmail.com>

.zenodo.json

@@ -58,7 +58,7 @@
     },
     {
       "affiliation": "Klinikum rechts der Isar, TUM. ACPySS",
-      "name": "Manh\u00e3es-Savio, Alexandre",
+      "name": "Manhães-Savio, Alexandre",
       "orcid": "0000-0002-6608-6885"
     },
     {
@@ -127,7 +127,7 @@
     },
     {
       "affiliation": "Stanford University",
-      "name": "\u0106iri\u0107 , Rastko",
+      "name": "Ćirić , Rastko",
       "orcid": "0000-0001-6347-7939"
     },
     {
@@ -214,7 +214,7 @@
       "name": "Tungaraza, Rosalia"
     },
     {
-      "affiliation": "Charit\u00e8 Universit\u00e4tsmedizin Berlin, Germany",
+      "affiliation": "Charitè Universitätsmedizin Berlin, Germany",
       "name": "Dell'Orco, Andrea",
       "orcid": "0000-0002-3964-8360"
     },
@@ -277,7 +277,7 @@
     },
     {
       "affiliation": "ARAMIS LAB, Brain and Spine Institute (ICM), Paris, France.",
-      "name": "Guillon, Je\u0301re\u0301my",
+      "name": "Guillon, Jérémy",
       "orcid": "0000-0002-2672-7510"
     },
     {
@@ -314,7 +314,7 @@
       "orcid": "0000-0001-9130-1092"
     },
     {
-      "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany",
+      "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany",
       "name": "Bernardoni, Fabio",
       "orcid": "0000-0002-5112-405X"
     },
@@ -324,15 +324,15 @@
       "orcid": "0000-0002-0805-1350"
     },
     {
-      "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universit\u00e4t Dresden, Dresden, Germany",
+      "affiliation": "Division of Psychological and Social Medicine and Developmental Neuroscience, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany",
       "name": "Geisler, Daniel",
       "orcid": "0000-0003-2076-5329"
     },
     {
       "name": "Salvatore, John"
     },
     {
-      "affiliation": "CNRS LTCI, Telecom ParisTech, Universit\u00e9 Paris-Saclay",
+      "affiliation": "CNRS LTCI, Telecom ParisTech, Université Paris-Saclay",
       "name": "Gramfort, Alexandre",
       "orcid": "0000-0001-9791-4404"
     },
@@ -392,13 +392,18 @@
       "name": "Liem, Franz",
       "orcid": "0000-0003-0646-4810"
     },
+    {
+      "affiliation": "ARAMIS Lab, Paris Brain Institute",
+      "name": "Vaillant, Ghislain",
+      "orcid": "0000-0003-0267-3033"
+    },
     {
       "affiliation": "Neurospin/Unicog/Inserm/CEA",
       "name": "Perez-Guevara, Martin Felipe",
       "orcid": "0000-0003-4497-861X"
     },
     {
-      "name": "Heinsfeld, Anibal S\u00f3lon",
+      "name": "Heinsfeld, Anibal Sólon",
       "orcid": "0000-0002-2050-0614"
     },
     {
@@ -417,7 +422,7 @@
       "name": "Poldrack, Russell"
     },
     {
-      "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montr\u00e9al, 3801 University Street, WB-208, H3A 2B4, Qu\u00e9bec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
+      "affiliation": "1 McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montréal, 3801 University Street, WB-208, H3A 2B4, Québec, Canada. 2 University of Lyon, CNRS, INSERM, CREATIS., Villeurbanne, 7, avenue Jean Capelle, 69621, France.",
       "name": "Glatard, Tristan",
       "orcid": "0000-0003-2620-5883"
     },
@@ -436,7 +441,7 @@
     },
     {
       "affiliation": "University College London",
-      "name": "P\u00e9rez-Garc\u00eda, Fernando",
+      "name": "Pérez-García, Fernando",
       "orcid": "0000-0001-9090-3024"
     },
     {
@@ -451,6 +456,11 @@
       "affiliation": "University of Iowa",
       "name": "Welch, David"
     },
+    {
+      "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
+      "name": "Ben-Zvi, Gal",
+      "orcid": "0000-0002-5655-9423"
+    },
     {
       "affiliation": "Max Planck Institute for Human Cognitive and Brain Sciences",
       "name": "Contier, Oliver",
@@ -476,7 +486,7 @@
     },
     {
       "affiliation": "Leibniz Institute for Neurobiology",
-      "name": "Stadler, J\u00f6rg",
+      "name": "Stadler, Jörg",
       "orcid": "0000-0003-4313-129X"
     },
     {
@@ -538,11 +548,6 @@
       "name": "Bielievtsov, Dmytro",
       "orcid": "0000-0003-3846-7696"
     },
-    {
-      "affiliation": "Sagol School of Neuroscience, Tel Aviv University",
-      "name": "Ben-Zvi, Gal",
-      "orcid": "0000-0002-5655-9423"
-    },
     {
       "affiliation": "University of Newcastle, Australia",
       "name": "Cooper, Gavin",
@@ -558,7 +563,7 @@
     },
     {
       "affiliation": "German Institute for International Educational Research",
-      "name": "Linkersd\u00f6rfer, Janosch",
+      "name": "Linkersdörfer, Janosch",
       "orcid": "0000-0002-1577-1233"
     },
     {
@@ -572,7 +577,7 @@
       "name": "Stanley, Olivia"
     },
     {
-      "name": "K\u00fcttner, Ren\u00e9"
+      "name": "Küttner, René"
     },
     {
       "affiliation": "California Institute of Technology",
@@ -700,11 +705,6 @@
       "name": "Lerma-Usabiaga, Garikoitz",
       "orcid": "0000-0001-9800-4816"
     },
-    {
-      "affiliation": "ARAMIS Lab, Paris Brain Institute",
-      "name": "Vaillant, Ghislain",
-      "orcid": "0000-0003-0267-3033"
-    },
     {
       "name": "Schwabacher, Isaac"
     },
@@ -730,7 +730,7 @@
       "orcid": "0000-0003-2077-3070"
     },
     {
-      "affiliation": "TIB \u2013 Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
+      "affiliation": "TIB – Leibniz Information Centre for Science and Technology and University Library, Hannover, Germany",
       "name": "Leinweber, Katrin",
       "orcid": "0000-0001-5135-5758"
     },
@@ -764,7 +764,7 @@
     },
     {
       "affiliation": "Universidad de Guadalajara",
-      "name": "Gonz\u00e1lez Orozco, Abel A."
+      "name": "González Orozco, Abel A."
     },
     {
       "affiliation": "ARAMIS Lab",

doc/changelog/1.X.X-changelog.rst

@@ -1,3 +1,45 @@
+1.8.3 (July 14, 2022)
+=====================
+
+Bug-fix release in the 1.8.x series.
+
+This release includes compatibility fixes for nibabel 4.x and resolves a denial-of-service
+bug when the etelemetry server is down that resulted in excessive (blocking) network hits that
+would cause any tools using nipype interfaces to take a very long time.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.8.3?closed=1>`__)
+
+  * FIX: Argument order to ``numpy.save()`` (https://github.com/nipy/nipype/pull/3485)
+  * FIX: Add tolerance parameter to ComputeDVARS (https://github.com/nipy/nipype/pull/3489)
+  * FIX: Delay access of nibabel.trackvis until actually needed (https://github.com/nipy/nipype/pull/3488)
+  * FIX: Avoid excessive etelemetry pings (https://github.com/nipy/nipype/pull/3484)
+  * ENH: Added outputs' generation to DWIBiascorrect interface (https://github.com/nipy/nipype/pull/3476)
+
+
+1.8.2 (June 06, 2022)
+=====================
+
+Bug-fix release in the 1.8.x series.
+
+This release restores compatibility with networkx 2.8.3, which errors when
+graph nodes might conflict with pydot parsing.
+
+(`Full changelog <https://github.com/nipy/nipype/milestone/1.8.2?closed=1>`__)
+
+  * ENH: Enable compression with Gunzip interface (https://github.com/nipy/nipype/pull/3472)
+  * CI: Schedule weekly tests with cron (https://github.com/nipy/nipype/pull/3480)
+
+
+1.8.1 (May 16, 2022)
+====================
+
+Bug-fix release in the 1.8.x series.
+
+The previous release vendored ``distutils.version.LooseVersion``, and the vendored objects did not
+preserve compatiblity with the ``distutils`` objects. This release switches to the
+``looseversion`` package that ensures compatiblity.
+
+
 1.8.0 (May 10, 2022)
 ====================
 

doc/interfaces.rst

@@ -8,7 +8,7 @@ Interfaces and Workflows
 :Release: |version|
 :Date: |today|
 
-Previous versions: `1.8.0 <http://nipype.readthedocs.io/en/1.8.0/>`_ `1.7.1 <http://nipype.readthedocs.io/en/1.7.1/>`_
+Previous versions: `1.8.2 <http://nipype.readthedocs.io/en/1.8.2/>`_ `1.8.1 <http://nipype.readthedocs.io/en/1.8.1/>`_
 
 Workflows
 ---------

nipype/__init__.py

@@ -14,7 +14,7 @@
 import os
 
 # XXX Deprecate this import
-from .external.version import LooseVersion
+from looseversion import LooseVersion
 
 from .info import URL as __url__, STATUS as __status__, __version__
 from .utils.config import NipypeConfig
@@ -98,4 +98,4 @@ def check_latest_version(raise_exception=False):
         from .interfaces.base import BaseInterface
 
         if BaseInterface._etelemetry_version_data is None:
-            BaseInterface._etelemetry_version_data = check_latest_version()
+            BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"

nipype/algorithms/confounds.py

@@ -50,6 +50,11 @@ class ComputeDVARSInputSpec(BaseInterfaceInputSpec):
     remove_zerovariance = traits.Bool(
         True, usedefault=True, desc="remove voxels with zero variance"
     )
+    variance_tol = traits.Float(
+        1e-7,
+        usedefault=True,
+        desc="maximum variance to consider \"close to\" zero for the purposes of removal",
+    )
     save_std = traits.Bool(True, usedefault=True, desc="save standardized DVARS")
     save_nstd = traits.Bool(False, usedefault=True, desc="save non-standardized DVARS")
     save_vxstd = traits.Bool(
@@ -167,6 +172,7 @@ def _run_interface(self, runtime):
             self.inputs.in_file,
             self.inputs.in_mask,
             remove_zerovariance=self.inputs.remove_zerovariance,
+            variance_tol=self.inputs.variance_tol,
             intensity_normalization=self.inputs.intensity_normalization,
         )
 
@@ -994,8 +1000,19 @@ def _list_outputs(self):
         return self._results
 
 
+def _AR_est_YW(x, order, rxx=None):
+    """Retrieve AR coefficients while dropping the sig_sq return value"""
+    from nitime.algorithms import AR_est_YW
+
+    return AR_est_YW(x, order, rxx=rxx)[0]
+
+
 def compute_dvars(
-    in_file, in_mask, remove_zerovariance=False, intensity_normalization=1000
+    in_file,
+    in_mask,
+    remove_zerovariance=False,
+    intensity_normalization=1000,
+    variance_tol=0.0,
 ):
     """
     Compute the :abbr:`DVARS (D referring to temporal
@@ -1027,36 +1044,35 @@ def compute_dvars(
     """
     import numpy as np
     import nibabel as nb
-    from nitime.algorithms import AR_est_YW
     import warnings
 
-    func = nb.load(in_file).get_fdata(dtype=np.float32)
-    mask = np.asanyarray(nb.load(in_mask).dataobj).astype(np.uint8)
+    func = np.float32(nb.load(in_file).dataobj)
+    mask = np.bool_(nb.load(in_mask).dataobj)
 
     if len(func.shape) != 4:
         raise RuntimeError("Input fMRI dataset should be 4-dimensional")
 
-    idx = np.where(mask > 0)
-    mfunc = func[idx[0], idx[1], idx[2], :]
+    mfunc = func[mask]
 
     if intensity_normalization != 0:
         mfunc = (mfunc / np.median(mfunc)) * intensity_normalization
 
     # Robust standard deviation (we are using "lower" interpolation
     # because this is what FSL is doing
     func_sd = (
-        np.percentile(mfunc, 75, axis=1, interpolation="lower")
-        - np.percentile(mfunc, 25, axis=1, interpolation="lower")
+        np.percentile(mfunc, 75, axis=1, method="lower")
+        - np.percentile(mfunc, 25, axis=1, method="lower")
     ) / 1.349
 
     if remove_zerovariance:
-        mfunc = mfunc[func_sd != 0, :]
-        func_sd = func_sd[func_sd != 0]
+        zero_variance_voxels = func_sd > variance_tol
+        mfunc = mfunc[zero_variance_voxels, :]
+        func_sd = func_sd[zero_variance_voxels]
 
     # Compute (non-robust) estimate of lag-1 autocorrelation
     ar1 = np.apply_along_axis(
-        AR_est_YW, 1, regress_poly(0, mfunc, remove_mean=True)[0].astype(np.float32), 1
-    )[:, 0]
+        _AR_est_YW, 1, regress_poly(0, mfunc, remove_mean=True)[0].astype(np.float32), 1
+    )
 
     # Compute (predicted) standard deviation of temporal difference time series
     diff_sdhat = np.squeeze(np.sqrt(((1 - ar1) * 2).tolist())) * func_sd