Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. 0.13.1

0.13.1 (May 20, 2017) FIX: Make release compatible with conda-forge build process (https://github.com/nipy/nipype/pull/2017) ENH: Update some minimum versions in compliance with Debian Jessie (https://github.com/nipy/nipype/pull/2017) ENH: Circle builds use cached docker layers (https://github.com/nipy/nipype/pull/2017) ENH: Base docker to use FS6 and ANTS 2.2.0 (https://github.com/nipy/nipype/pull/2024) FIX: Mailmap and contributor acknowledgment (https://github.com/nipy/nipype/pull/2017) FIX: Preserve node properties in sub nodes of MapNode (https://github.com/nipy/nipype/pull/2019) FIX: Fix interfaces 3DUnifize, ICA_AROMA, BinaryMaths, RegAverage, BBRegister, AffineInitializer (https://github.com/nipy/nipype/pull/2025, https://github.com/nipy/nipype/pull/2027, https://github.com/nipy/nipype/pull/2036, https://github.com/nipy/nipype/pull/2037, https://github.com/nipy/nipype/pull/2031, https://github.com/nipy/nipype/pull/2010) ENH: Add Anisotropic Power interface (https://github.com/nipy/nipype/pull/2039) FIX: Bayesian estimation in SPM (https://github.com/nipy/nipype/pull/2030) 0.13.0 (May 11, 2017) ENH: Multi-stage recon-all directives (https://github.com/nipy/nipype/pull/1991) FIX: FEAT "folder does not exist" error (https://github.com/nipy/nipype/pull/2000) ENH: Niftyfit interfaces (https://github.com/nipy/nipype/pull/1910) FIX: Define ANTSPATH for BrainExtraction automatically (https://github.com/nipy/nipype/pull/1986) ENH: New trait for imaging files (https://github.com/nipy/nipype/pull/1949) ENH: Niftyseg interfaces (https://github.com/nipy/nipype/pull/1911) ENH: Niftyreg interfaces (https://github.com/nipy/nipype/pull/1913) MRG: Allow more support for CLI (https://github.com/nipy/nipype/pull/1908) ENH: 3dQwarpPlusMinus interface (https://github.com/nipy/nipype/pull/1974) FIX: PY3.6 support (https://github.com/nipy/nipype/pull/1977) FIX: PY3 and stream fixes for MRTrix2TrackVis (https://github.com/nipy/nipype/pull/1804) ENH: More mask options for CompCor interfaces (https://github.com/nipy/nipype/pull/1968 + https://github.com/nipy/nipype/pull/1992) ENH: Additional TOPUP outputs (https://github.com/nipy/nipype/pull/1976) ENH: Additional Eddy flags (https://github.com/nipy/nipype/pull/1967) ENH: ReconAll handlers for less common cases (https://github.com/nipy/nipype/pull/1966) ENH: FreeSurferSource now finds graymid/midthickness surfs (https://github.com/nipy/nipype/pull/1972) ENH: Additional fslmaths dimensional reduction operations (https://github.com/nipy/nipype/pull/1956) ENH: More options for RobustFOV interface (https://github.com/nipy/nipype/pull/1923) ENH: Add MRIsCombine to FreeSurfer utils (https://github.com/nipy/nipype/pull/1948) FIX: Level1Design EV parameter substitution (https://github.com/nipy/nipype/pull/1953) FIX: Dcm2niix outputs can be uncompressed (https://github.com/nipy/nipype/pull/1951) FIX: Ensure build fails in Circle when tests fail (https://github.com/nipy/nipype/pull/1981) ENH: Add interface to antsAffineInitializer (https://github.com/nipy/nipype/pull/1980) ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840) ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845) FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (https://github.com/nipy/nipype/pull/1728) FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871) FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875) DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881) ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886) FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890) ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893) FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894) FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903) FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907) FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917) ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918) FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926) DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930) ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924) ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941) ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896) ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839) ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811) REF: Splits nipype.interfaces.utility into base, csv, and wrappers (https://github.com/nipy/nipype/pull/1828) FIX: Makespec now runs with nipype in current directory (https://github.com/nipy/nipype/pull/1813) FIX: Flexible nifti opening with mmap if Numpy < 1.12.0 (https://github.com/nipy/nipype/pull/1796 + https://github.com/nipy/nipype/pull/1831) ENH: DVARS includes intensity normalization feature - turned on by default (https://github.com/nipy/nipype/pull/1827) FIX: DVARS is correctly using sum of squares instead of standard deviation (https://github.com/nipy/nipype/pull/1827) ENH: Refactoring of nipype.interfaces.utility (https://github.com/nipy/nipype/pull/1828) FIX: CircleCI were failing silently. Some fixes to tests (https://github.com/nipy/nipype/pull/1833) FIX: Issues in Docker image permissions, and docker documentation (https://github.com/nipy/nipype/pull/1825) ENH: Revised all Dockerfiles and automated deployment to Docker Hub from CircleCI (https://github.com/nipy/nipype/pull/1815) ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790) FIX: Cast DVARS float outputs to avoid memmap error (https://github.com/nipy/nipype/pull/1777) FIX: FSL FNIRT intensity mapping files (https://github.com/nipy/nipype/pull/1799) ENH: Additional outputs generated by FSL EDDY (https://github.com/nipy/nipype/pull/1793) TST: Parallelize CircleCI build across 4 containers (https://github.com/nipy/nipype/pull/1769) 0.13.0-rc1 (January 4, 2017) FIX: Compatibility with traits 4.6 (https://github.com/nipy/nipype/pull/1770) FIX: Multiproc deadlock (https://github.com/nipy/nipype/pull/1756) TST: Replace nose and unittest with pytest (https://github.com/nipy/nipype/pull/1722, https://github.com/nipy/nipype/pull/1751) FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689) REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680) ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608) FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669) FIX: Minor errors after migration to setuptools (https://github.com/nipy/nipype/pull/1671) ENH: Add AFNI 3dNote interface (https://github.com/nipy/nipype/pull/1637) ENH: Abandon distutils, only use setuptools (https://github.com/nipy/nipype/pull/1627) FIX: Minor bugfixes related to unicode literals (https://github.com/nipy/nipype/pull/1656) TST: Automatic retries in travis (https://github.com/nipy/nipype/pull/1659/files) ENH: Add signal extraction interface (https://github.com/nipy/nipype/pull/1647) ENH: Add a DVARS calculation interface (https://github.com/nipy/nipype/pull/1606) ENH: New interface to b0calc of FSL-POSSUM (https://github.com/nipy/nipype/pull/1399) ENH: Add CompCor (https://github.com/nipy/nipype/pull/1599) ENH: Add duecredit entries (https://github.com/nipy/nipype/pull/1466) FIX: Python 3 compatibility fixes (https://github.com/nipy/nipype/pull/1572) REF: Improved PEP8 compliance for fsl interfaces (https://github.com/nipy/nipype/pull/1597) REF: Improved PEP8 compliance for spm interfaces (https://github.com/nipy/nipype/pull/1593) TST: Replaced coveralls with codecov (https://github.com/nipy/nipype/pull/1609) ENH: More BrainSuite interfaces (https://github.com/nipy/nipype/pull/1554) ENH: Convenient load/save of interface inputs (https://github.com/nipy/nipype/pull/1591) ENH: Add a Framewise Displacement calculation interface (https://github.com/nipy/nipype/pull/1604) FIX: Use builtins open and unicode literals for py3 compatibility (https://github.com/nipy/nipype/pull/1572) TST: reduce the size of docker images & use tags for images (https://github.com/nipy/nipype/pull/1564) ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563) FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586) ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582) ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant (https://github.com/nipy/nipype/pull/1654

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (vol 52, pg 331, 2020)

author correctio