MRtrix3 Nightly release

Merge pull request #3246 from MRtrix3/fix_mac_packaging

Fixes for macOS packaging build script

MRtrix3 release 3.0.8

Eighth micro (bug fix) update to fix issues identified in previous release, and fix longstanding issues with MRView on macOS.

What's Changed

• Testing: Relax tolerances on fixelcfestats tests by @Lestropie in #3149
• mrmath: Typo in error message by @Lestropie in #3150
• Fix phase encoding handling on 3.0.7 by @Lestropie in #3146
• MR::Axes::permutations_type: Fix is_identity() by @Lestropie in #3169
• fsl.check_first(): Handle run_first_all providing no HOLDID by @Lestropie in #3176
• Pipe image format: Revise error message by @Lestropie in #3154
• mrcalc: Docs: Combining mag&phase into complex data by @Lestropie in #3148
• mesh2voxel: Accept >3D image as template voxel grid by @Lestropie in #3107
• tck2connectome: Add default assignment mechanism to docs by @Lestropie in #3181
• Fix Eigen 3.4.1 type mismatch in ColourMap clamping by @daljit46 in #3207
• Update configure script for Xcode26 compatibility by @bjeurissen in #3202
• DICOM: Performance fix to wildcard matching by @Lestropie in #3208
• Fix ROI edits disappearing on MacOS by @daljit46 in #3195
• Fix tractography rendering performance on macOS by @daljit46 in #3197
• tcksift2 & afdconnectivity: Update citation by @Lestropie in #3205
• Stats commands: Clarify non-stationarity correction in help pages by @Lestropie in #3187
• tcksift2: Minor fixes to diagnosis data by @Lestropie in #3050
• Docs: Description of options with single-shell data by @Lestropie in #3198
• tckglobal: Disable multi-threading by default by @Lestropie in #3194
• mrview: Bugfix in rendering of cubes in connectome tool by @Lestropie in #3204
• Fix race condition in ThreadedLoop by @jdtournier in #3215
• tckglobal: Fix operation by @Lestropie in #3172
• Next release 3.0.8 by @jdtournier in #3222
• next release 3.0.8 - take 2 by @jdtournier in #3225

Full Changelog: 3.0.7...3.0.8

MRtrix3 release 3.0.7

Seventh micro (bug fix) update to fix issues identified in previous release.

Please consult the main announcement and summary of changes for details.

---

What's Changed

• Generate correct applytopup_config.txt by @bjeurissen in #3123
• Fixes to external phase encoding table handling by @Lestropie in #3128
• dwifslpreproc & mrcat: Strides fix by @Lestropie in #2806
• mrview: Fix typo in help page by @Lestropie in #3136
• next release 3.0.7 by @jdtournier in #3138

Full Changelog: 3.0.6...3.0.7

MRtrix3 release 3.0.6

Sixth micro (bug fix) update to fix regression introduced in previous release.

Full changelog

Bug fixes

• Fix erroneous clamping of FSL bvals
  Code error introduced in the merge commit of changes in #2602, which will cause problems when using -export_grad_fsl on any DWI with more than 3 volumes.

• Suppress erroneous warning RE merging of gradient table
  Even if concatenating two 4D series along the volume axis, where the two gradient tables should be stacked atop one another, mrcat produces a warning about an inability to merge gradient tables. The appropriately concatenated gradient table would still be present in the output image, it would just be an erroneous warning at the terminal.

Installation

• Fix error during Conda install
  Fixes errors during Conda install that affect GitHub Action runners, as reported on the community forum

Build/debug refinements

• Fixes for sanitisers workflow
  The weekly sanitisers workflow is missing the installation of libpng-dev, which is causing the mrconvert_format_png test to fail.

• tck2connectome: Fix erroneous assertion with -vector
  Only prevents erroneous assertion failure; this will have no effect on processing results in release mode.

---

What's Changed

• Revert container recipes to pull master by @jdtournier in #3093
• tck2connectome: Fix erroneous assertion with -vector by @Lestropie in #3095
• Fixes for sanitisers workflow by @daljit46 in #3081
• Fix erroneous clamping of FSL bvals by @Lestropie in #3112
• Suppress erroneous warning RE merging of gradient table by @Lestropie in #3106
• Next release 3.0.6 by @jdtournier in #3117

Detailed Changelog: 3.0.5...3.0.6

MRtrix3 release 3.0.5

Fifth micro (bug fix) update following initial production release.

Please consult the main announcement and summary of changes for details.

What's Changed

• show correct version in symlinked python scripts by @jdtournier in #2548
• Revert container recipes to pull master by @jdtournier in #2544
• DICOM: Tweak terminal messages by @Lestropie in #2549
• Update Copyright notice for 2023 by @dchristiaens in #2555
• resize instead of assign of std::vector by @bjeurissen in #2568
• python library: tweak execute to work with VS Code #2472 by @Lestropie in #2566
• Fix sprintf deprecation warning on macOS by @bjeurissen in #2561
• mrview: change option name -orientationlabel to avoid conflict with -orientation by @jdtournier in #2569
• Revert "mrview: change option name -orientationlabel to avoid conflict with -orientation" by @jdtournier in #2581
• Update GitHub Actions workflow for merge queue by @jdtournier in #2588
• Add file ".git-blame-ignore-revs" by @Lestropie in #2592
• VTK surface format changes by @Lestropie in #2594
• App::get_matches(): Fix buffer overrun by @Lestropie in #2629
• Mesh::load_vtk() always open files in binary mode by @jdtournier in #2656
• mrview: fix tsf custom colour by @jdtournier in #2667
• tcksift2: Fix check for allocation of memory for weights vector by @Lestropie in #2672
• DICOM: fix multiframe encoding with explicit length sequences by @jdtournier in #2691
• Docs: Explicitly specify English language to Sphinx by @Lestropie in #2715
• ReadTheDocs: updates to fix render by @jdtournier in #2727
• add support for python importlib to locate MRtrix3 python libraries by @jdtournier in #2735
• configure: revert to -isystem rather than -idirafter by @jdtournier in #2754
• Update header copyright to 2024 by @Lestropie in #2771
• Allow filename in write_mrtrix.m to be string or char array by @lukeje in #2810
• Docs: New page on MRView "lock to image axes" by @Lestropie in #2882
• CI: Fixes for MacOSX ARM64 runner by @Lestropie in #2890
• Adapter::Reslice: Alternative resolution of complex summation by @Lestropie in #2785
• Reslice adapter: allow use with complex numbers by @jdtournier in #2768
• Add periodic checks with sanitizers by @daljit46 in #2763
• mrgrid: Fix help for -as option by @Lestropie in #2794
• run.command(): Do not hide list inputs by @Lestropie in #2803
• for_each: Add example usage demonstrating shell operator escape by @Lestropie in #2721
• mrinfo: Update author email by @Lestropie in #2698
• fod2fixel: Fix -fmls_lobe_merge_ratio by @Lestropie in #2638
• Update sanitizers workflow following testing changes by @daljit46 in #2904
• mrcalc: Support -config option by @Lestropie in #2910
• mrdegibbs: update doc to soften warning about partial Fourier by @jdtournier in #2923
• ProgressBar: Simple update method where stderr is pipe by @Lestropie in #2935
• New workflow for releases by @daljit46 in #2933
• Deprecated distutils module in Python 3.12 by @Lestropie in #2948
• Windows: Delayed writeback to host by @Lestropie in #2962
• Pipe image format: Revise error message by @Lestropie in #2600
• dwi2tensor: Preserve dw_scheme for -predicted_signal by @Lestropie in #2955
• DICOM command-line selection: abort on error reading from std::cin by @Lestropie in #2908
• population_template: Fix aggregation weights import by @Lestropie in #3001
• Python: Pylint fix consider-using-generator by @Lestropie in #3005
• Docs: Fix missing boolean types in full usage by @Lestropie in #2693
• PNG: Fix check for too few axes, memory, orientations by @Lestropie in #2713
• 5ttcheck: Fix terminal message RE: -voxels option by @Lestropie in #2411
• configure: strip FSL from PATH by @jdtournier in #2729
• Fix for mrview / singularity / NVIDIA by @celstark in #2559
• Fixes to containers FSL dependency by @Lestropie in #2929
• [ENH] Update Dockerfile by @arnaudbore in #3039
• Pylint fixes for master branch by @Lestropie in #3054
• Added info about consequences of using -white_stem in 5ttgen hsvs by @Lestropie in #3042
• dwifslpreproc: Fix for PE direction, but not readout time, in header by @Lestropie in #2722
• mrtrix3.path.wait_for(): Fix variable ghosting by @Lestropie in #2968
• voxel2mesh fixes by @Lestropie in #3049
• dwi2tensor: fix operation with -iter 1 by @Lestropie in #3056
• DICOM: add null imageIO handler to allow parsing of DICOM data even with unsupported transfer syntax by @jdtournier in #2767
• Tolerance for dw_scheme differences on header merge by @Lestropie in #3027
• DICOM: ignore image positioning tags if nested within Philips private sequence by @jdtournier in #3047
• Fix tck writer when a single streamline exceed the buffer size by @jdtournier in #3071
• DWI metadata fixes for master by @Lestropie in #3011
• fsl.check_first(): Second attempt at refinement by @Lestropie in #2609
• More robust bvecs/bvals compatibility by @Lestropie in #2602
• Fix packaging workflows on master by @daljit46 in #3086
• Final GA workflows changes for 3.0.5 by @daljit46 in #3091
• Next release 3.0.5 by @jdtournier in #3092

New Contributors

• @lukeje made their first contribution in #2810
• @celstark made their first contribution in #2559
• @arnaudbore made their first contribution in #3039

Full Changelog: 3.0.4...3.0.5

MRtrix3 release 3.0.4

Fourth micro (bug fix) update following initial production release.

Please consult the main announcement and summary of changes for details.

What's Changed

• Revert container recipes to pull master by @Lestropie in #2357
• CONTRIBUTING.md: Revise by @Lestropie in #2358
• Eigen 3.4 compatibility by @jdtournier in #2368
• dwicat: Support 3D images by @Lestropie in #2366
• add .nojekyll file to documentation update script by @jdtournier in #2384
• dwifslpreproc: strip DW encoding from padding slice by @jdtournier in #2382
• dwi2response manual: avoid checking and calculating a brain mask by @bjeurissen in #2373
• README.md: Add Twitter reference by @Lestropie in #2395
• Documentation (Fixels and Dixels): double negative typo by @fionaEyoung in #2398
• minimal set of changes to pass pylint 2.11.1 tests by @jdtournier in #2401
• Fix link to advanced debugging help page by @fionaEyoung in #2403
• CONTRIBUTING.md: Revise text RE: target branch for docs changes by @Lestropie in #2402
• Update copyright and docs by @jdtournier in #2425
• tensor2metric: avoid crash when supplying input with wrong size by @bjeurissen in #2423
• Avoid invalid memory access when ROI is malformed in tck header by @jdtournier in #2424
• mrtrix3.run: Fix default MRTRIX_LOGLEVEL by @Lestropie in #2432
• configure: ignore CFLAGS & LDFLAGS from qmake by @jdtournier in #2445
• tcksift2: Fix fixel masking by @Lestropie in #2447
• connectomestats: Fix GLM mode selection by @Lestropie in #2454
• Matlab: multiline key-value metadata #2386 by @fionaEyoung in #2455
• connectomestats: Fix output paths for some files by @Lestropie in #2453
• Various DICOM updates - take 2 with updated test data by @jdtournier in #2450
• mrtrix3.utils.RunList: Pass kwargs to run.command() by @Lestropie in #2209
• Dicom fix XA10A parsing by @jdtournier in #2462
• Container: Additional fixes by @Lestropie in #2461
• Dicom fix missing import siemens enhanced by @jdtournier in #2466
• Fixes incorrect face orientation in PLY output format by @blezek in #2490
• mrview connectome tool: fix display of nodes when a node is empty by @jdtournier in #2497
• Correctly transform mask instead of last contrast by @bjeurissen in #2503
• mrtransform: DWI grad export on linear by @Lestropie in #2508
• Write separate std_dev for each variance group by @bjeurissen in #2507
• mrview: Permit SH lmax=0 by @bjeurissen in #2511
• Fix build progress by @jdtournier in #2494
• Tckconvert write binary vtk by @jdtournier in #2489
• Python: don't cleanup on SIGINT if -nocleanup option has been provided by @jdtournier in #2484
• update mime & icon handling on linux by @jdtournier in #2478
• matlab: Fix erroneous reference to non-existent "tracks" identifier by @fionaEyoung in #2522
• dwifslpreproc: Refine slspec modification by @Lestropie in #2505
• Container recipe updates following 3.0.3 release by @Lestropie in #2370
• mrview: improved error reporting in fixel plot tool by @tbschuster in #2367
• GitHub Actions: fix dependencies on Ubuntu 22.04 by @jdtournier in #2532
• DICOM: fix parsing of DateTime entry by @jdtournier in #2531
• PNG export: Exception on too few axes by @Lestropie in #2535
• mrview fix tractography.tsf_colourmap by @maxpietsch in #2452
• DICOM: fix import of gradient table by @jdtournier in #2523
• Final checks before 3.0.4 release by @jdtournier in #2543

Full Changelog: 3.0.3...3.0.4

MRtrix3 release 3.0.3

Third micro (bug fix) update following initial production release.

Please consult the main announcement and summary of changes for details.

What's Changed

• labelconvert: Error if -spine used but absent from LUT by @Lestropie in #2187
• Docs: afdconnectivity: Link to preprint by @Lestropie in #2201
• MGH/MGZ: Fix Colortable V2 write by @Lestropie in #2216
• Docs: DW handling: Describe shells by @Lestropie in #2194
• Pylint fixes for master by @Lestropie in #2204
• dwifslpreproc: Fix for rare usage by @Lestropie in #2229
• dwidenoise: limit patch size to image dimensions by @dchristiaens in #2230
• dwifslpreproc: fix help for -align_seepi option by @jdtournier in #2236
• Minor command docs updates by @Lestropie in #2242
• dwifslpreproc: On -rpe_pair, ensure -se_epi is 4D by @Lestropie in #2244
• Fixes issue when double-clicking quarantined files on macos. by @bjeurissen in #2246
• Changes to pass CI: update copyright notice and remove redundant homebrew fixes by @jdtournier in #2251
• dwi2response dhollander: fix handling of data with negative values by @jdtournier in #2252
• tckglobal: Fix bug that caused particles in a voxel to be duplicated when tried to be removed by @sertopexamgio in #2257
• tckglobal: Fix erroneous -niter parsing for values bigger that 1.4e9 by @sertopexamgio in #2258
• Inference: Fix for exotic usage by @Lestropie in #2260
• mrview: fix handling of -focus and -target options by @jdtournier in #2250
• python: fix handling of N/A output in image.statistics() by @jdtournier in #2249
• dirorder: Fix segfault by @Lestropie in #2272
• add two new command lines option in mrview for tractogram by @valeryozenne in #2290
• mrview: fix glitch in handling of clip plane selection by @jdtournier in #2291
• Fix help page for algorithm module by @Lestropie in #2293
• GLM: Fix all_stats() segfault by @Lestropie in #2294
• mrregister: fix lmax check for nonlinear multi contrast registration by @maxpietsch in #2300
• mrview: deactivate pan gesture to avoid #761 by @maxpietsch in #2310
• dwifslpreproc: Handle non-ascii data in eddy error outputs by @Lestropie in #2313
• Container recipes by @Lestropie in #2279
• dwifslpreproc: Fix eddy text file outputs (again) by @Lestropie in #2318
• New envvar MRTRIX_LOGLEVEL by @Lestropie in #2316
• DICOM: fix formatting error in dictionary by @jdtournier in #2324
• Update connectome2tck.cpp by @nicdc in #2327
• dwishellmath: Compatibility with one unique b-value by @Lestropie in #2288
• mrview: accept drop events by @maxpietsch in #2342
• configure: Add libpng envvars to usage string by @Lestropie in #2343
• mrview Overlay: Fix segfault on bad image load by @Lestropie in #2347
• Compatibility with Pylint 2.8 by @Lestropie in #2317
• dwifslpreproc: Fix to b=0 volume matching by @Lestropie in #2262
• population_template: replace whitespace in unique filename by @maxpietsch in #2213
• for_each: Fix use of regex for entry exclusion by @Lestropie in #2277
• Transparently handle UTF-8 dashes as regular ones by @jdtournier in #2193
• DICOM: simplify handling of parsing in context of multi-frame by @jdtournier in #2311
• Attempted fixes to phase encoding handling by @Lestropie in #2308
• preserve b-value scaling for b-zero #2231 by @dchristiaens in #2329
• dwifslpreproc: Compatibility between image padding and EddyQC by @Lestropie in #2286
• DICOM improvements by @jdtournier in #2346
• dwigradcheck: explain how to obtain corrected gradient table by @bjeurissen in #2321
• mrview: elide ODF file names by @maxpietsch in #2334
• mtnormalise: add resilience to non-finite values in mask by @jdtournier in #2298
• Fix script tests on master by @Lestropie in #2287
• mrview: fix volume index reset after image switch by @jdtournier in #2352
• docs: explicitly state to avoid Qt6 if building from source by @jdtournier in #2353
• Fixes the overlay colour map inversion gui bug by @tbschuster in #2354
• Release 3.0.3 (take 2) by @Lestropie in #2356

New Contributors

• @sertopexamgio made their first contribution in #2257
• @valeryozenne made their first contribution in #2290
• @nicdc made their first contribution in #2327

Full Changelog: 3.0.2...3.0.3

MRtrix3 release 3.0.2

Second micro (bug fix) update following initial production release version 3.0.0

Please consult the main announcement and summary of changes for details.

What's Changed

• dwifslpreproc: Fix eddy_quad susceptibility field by @Lestropie in #2127
• don't use QWheelEvent::pixelDelta() on Qt<5.5 by @jdtournier in #2122
• Fix matlab write mrtrix by @jdtournier in #2128
• Pipe handler: ensure deletion of piped images even if not loaded by @jdtournier in #2125
• dwi2fod: fix error when volumes not assigned to shells by @jdtournier in #2132
• Stats commands: Fix -strong option by @Lestropie in #2137
• mrtransform: Prevent erroneous warning by @Lestropie in #2141
• NIfTI2: Fix read following #1540 by @Lestropie in #2147
• run_tests: allow different location for MRtrix executables by @jdtournier in #2118
• Docs: State Qt5 as GUI requirement by @Lestropie in #2153
• mrgrid: ensure no oversampling when using nearest-neighbour interpolation by @jdtournier in #2159
• Remove copy_ptr and fix handling of masks when more than 3D by @jdtournier in #2162
• dwibiascorrect fsl: Revise warning by @Lestropie in #2171
• resize filter, adapter and reslice adapter: more explicit nearest interpolation and oversample handling by @maxpietsch in #2163
• dwifslpreproc: For EddyQC, don't invoke Python3 interpreter by @Lestropie in #2166
• Tweak error message on failed fixel overwrite by @Lestropie in #2173
• convert_bruker: fix DW scheme handling by @jdtournier in #2178
• mrhistmatch: Use normal equation by @Lestropie in #2184
• [BUG] tckgen: Fix absent CST with ACT by @Lestropie in #2180
• NIfTI: Fix verification of rigid transform by @Lestropie in #2185
• 3.0.2 release for final CI testing by @jdtournier in #2186

Full Changelog: 3.0.1...3.0.2

MRtrix3 release 3.0.1

First micro update following initial production release version 3.0.0

Please consult the main announcement and summary of changes for details.

What's Changed

• Android fixes by @bjeurissen in #2044
• Math::Zstatistic: Fix compiler warning by @Lestropie in #2054
• Copyright by @Lestropie in #2053
• CohortDataImport::initialise(): Fix for cwd by @Lestropie in #2057
• Add .gitattributes file by @dchristiaens in #2051
• dwifslpreproc: add missing reorient_fod option by @bjeurissen in #2062
• progressbar: fix behaviour under redirection by @jdtournier in #2061
• dwifslpreproc: Don't discard modified dw_scheme by @Lestropie in #2067
• mtnormalise: warn if only one contrast provided by @maxpietsch in #2070
• Updates to installation documentation by @jdtournier in #2049
• dwifslpreproc: eddy error message by @Lestropie in #2073
• Fix line endings in src/gui/mrview/sync/enums.h by @Lestropie in #2081
• Merge master hotfixes into dev by @Lestropie in #2082
• Fix compiler warnings by @Lestropie in #2080
• mrview: add viridis colour maps and fix PET colour map by @dchristiaens in #2089
• fixelfilter: Remove erroneous DESCRIPTION statement by @Lestropie in #2093
• tckgen: Fix enabling DEBUG_TERMINATIONS by @Lestropie in #2077
• Simplify gl_core header by @jdtournier in #2060
• tckgen: fix mean number of samples: NaN for iFOD2 by @jdtournier in #2071
• Merge latest master changes into dev by @Lestropie in #2095
• mrthreshold: Suppress progressbars if writing to cout by @Lestropie in #2096
• run_tests: Permit running with manually-downloaded test data by @Lestropie in #2100
• Support FreeSurfer 7 LUT by @Lestropie in #2076
• mrview Tractography tool: Multiple fixes by @Lestropie in #2068
• dwifslpreproc: Fix overwrite of output eddy_quad directory by @Lestropie in #2105
• write_mrtrix.m: Fix syntax by @Lestropie in #2094
• docs: replace mrresize by mrgrid by @maxpietsch in #2114
• Support images with axis size greater than 2^31 by @Lestropie in #2113
• mrconvert: Update dw_scheme on -bvalue_scaling by @Lestropie in #2042
• Docs: Move fixel format to dedicated page in FBA by @Lestropie in #2109
• 3.0.1 update dev -> master by @Lestropie in #2115

Full Changelog: 3.0.0...3.0.1

MRtrix3 release 3.0.0

This is the first production release of MRtrix3, version 3.0.0

Please consult the main announcement and summary of changes for details.

What's Changed

• tckgen: Premature exit mechanism by @Lestropie in #832
• Explicit system signal handlers by @Lestropie in #776
• New fixel format by @draffelt in #823
• New function DWI::stash_DW_scheme() by @Lestropie in #774
• ZSH & amp2response by @Lestropie in #786
• Integrating amp2response in dwi2response scripts by @thijsdhollander in #862
• Copyright for 2017 in headers by @thijsdhollander in #891
• Proposed solution for Eigen alignment issues by @jdtournier in #883
• dwiextract: preserve DW scheme information exactly as per input by @jdtournier in #888
• Shview enhancements by @thijsdhollander in #894
• Documentation restructure by @draffelt in #890
• Script redesign by @Lestropie in #898
• Repo fhs restructure by @jdtournier in #896
• Registration: debug images and repeated stages by @maxpietsch in #913
• allocator alignment: use std::max_align_t rather than configure test by @jdtournier in #914
• Scripts: Better handling of scripts invoking other scripts by @Lestropie in #920
• Investigate missing max align t by @jdtournier in #917
• More fixes for scripts run.command() in 0.3.16 by @Lestropie in #922
• fixel2voxel: New option -number by @Lestropie in #923
• mrview view tool: buttons to copy voxel and scanner location to clipboard by @maxpietsch in #939
• mrview: outside FOV: set value_min and value_max to zero by @maxpietsch in #943
• Dwigradcheck by @Lestropie in #947
• Eigen OpenMP handling by @dchristiaens in #938
• Scripts: add version to man page by @maxpietsch in #951
• tckgen interface changes by @thijsdhollander in #921
• replace make_shared() by @jdtournier in #960
• mrinfo: -property: print key and indentation to stderr unless -quiet by @maxpietsch in #963
• Update to new tckgen option select by @rdpauw in #965
• file.waitfor(): Make more robust by @Lestropie in #969
• add current command-line to 'command_history' header entry by @jdtournier in #962
• Tag 0.3.16 by @Lestropie in #785
• Remove Anaconda from PATH. by @dchristiaens in #976
• mrconvert fix axis insertion #977 by @maxpietsch in #978
• Fix small mistake in image.py by @bjeurissen in #983
• docs: removed dirty page from display issues by @maxpietsch in #981
• Support Python3 scripts with -version option by @bjeurissen in #982
• PLY writer for tractography "streamlines" by @blezek in #967
• docs update by @thijsdhollander in #986
• Prevent estimation of optimal threshold when user specifies value by @blezek in #979
• package_mrtrix updated: stripped release, scripts-->bin. by @maxpietsch in #988
• Allow custom topup options as well by @bjeurissen in #990
• doc and copyright updates by @thijsdhollander in #991
• Threads: check that casting uint8_t to std::atomic<uint8_t> is safe by @jdtournier in #989
• Better reporting for unsupported dicom transfer syntax by @jdtournier in #995
• Fix segfault in global tractography. by @dchristiaens in #998
• mrregister: clarify smoothing default values by @maxpietsch in #1001
• docs update by @thijsdhollander in #1002
• Mtbin fixes by @thijsdhollander in #1003
• Move memory aligned deque to core/types.h by @dchristiaens in #999
• mtbin: fix isfinite check by @maxpietsch in #1004
• Mrview fix command line parsing by @maxpietsch in #1007
• MGH / MGZ: alternative implementation using normal file-based IO by @jdtournier in #970
• tckgen: More verbose description of tracking algorithms by @Lestropie in #1008
• dwipreproc: Additional instructions for -topup_options and -eddy_options by @Lestropie in #1009
• Improve matlab import code by @jdtournier in #1005
• dwipreproc: Fix variable naming error by @Lestropie in #1015
• Check for apps where image must be 3D by @Lestropie in #1017
• fix warnings about signed/unsigned comparisons by @jdtournier in #1018
• Read VTK as input streamlines, write RIB files (RenderMan) by @blezek in #997
• mrconvert: -axes option now also swaps voxel sizes as expected by @jdtournier in #1019
• mrconvert PE export with -coord option by @dchristiaens in #1022
• 5ttgen fsl improved waitfor by @Lestropie in #1020
• app.debug(): Enhance by @Lestropie in #1021
• Fixelcrop fix by @Lestropie in #1027
• tckconvert: add Daniel Blezek to the authors list by @jdtournier in #1028
• mrconvert: don't set PE scheme if PhaseEncoding::set_scheme throws an exception by @maxpietsch in #1031
• Tiff image format by @jdtournier in #1025
• fix compilation error on g++ 7.1 due to legacy code by @jdtournier in #1035
• Detect lustre to avoid memory mapping files by @CanWood in #1040
• GZ handling: use actual error string rather than assuming out of memory by @jdtournier in #1045
• package_mrtrix: update script by @jdtournier in #1046
• Silence compilation warnings on GCC7 by @Lestropie in #1041
• fixelcfestats: New option -mask by @Lestropie in #1030
• mtlognorm by @thijsdhollander in #1036
• fixed calculation of energy by @kpannek in #1050
• Ensure stat is 64-bit on Windows by @bjeurissen in #1060
• Dwipreproc & PhaseEncoding handling fixes by @Lestropie in #1047
• image_diff: relax tolerance on vox spacing by @jdtournier in #1059
• Tensor2metric sort by abs eigval by @jdtournier in #1026
• write_mrtrix: update to output generic fields by @jdtournier in #1063
• Dicom split series by image type by @jdtournier in #1056
• Tractography::Properties::get_step_size() function by @Lestropie in #1069
• mrtransform: add -oversample option by @jdtournier in #1067
• 5ttgen fsl: Fixes by @Lestropie in #1070
• Docs: Update advanced debugging page for 3.0_RC1 by @Lestropie in #1076
• dwipreproc: Fix volume matching with zero-length gradient vectors by @Lestropie in #1077
• MRView: Lightbox: View volumes of 4d image by @rtabbara in #694
• Added command options for mrview: by @LeeReid1 in #961
• new mrdegibbs command by @jdtournier in #1079
• Python fsl.findimage() function by @Lestropie in #1080
• Handle shell selection when using msmt_csd by @bjeurissen in #1082
• Tag 3.0 RC2 by @Lestropie in #1052
• dwi2mask: Fix for low image intensities by @Lestropie in #1083
• mrview Tractography tool: Fix to ...