Effect of slice thickness on brain magnetic resonance image texture analysis

Background The accuracy of texture analysis in clinical evaluation of magnetic resonance images depends considerably on imaging arrangements and various image quality parameters. In this paper, we study the effect of slice thickness on brain tissue texture analysis using a statistical approach and classification of T1-weighted images of clinically confirmed multiple sclerosis patients. Methods We averaged the intensities of three consecutive 1-mm slices to simulate 3-mm slices. Two hundred sixty-four texture parameters were calculated for both the original and the averaged slices. Wilcoxon's signed ranks test was used to find differences between the regions of interest representing white matter and multiple sclerosis plaques. Linear and nonlinear discriminant analyses were applied with several separate training and test sets to determine the actual classification accuracy. Results Only moderate differences in distributions of the texture parameter value for 1-mm and simulated 3-mm-thick slices were found. Our study also showed that white matter areas are well separable from multiple sclerosis plaques even if the slice thickness differs between training and test sets. Conclusions Three-millimeter-thick magnetic resonance image slices acquired with a 1.5 T clinical magnetic resonance scanner seem to be sufficient for texture analysis of multiple sclerosis plaques and white matter tissue.BioMed Central Open acces

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