Author Commit Message Commit Date Thijs Dhollander 2d1c38518e6 M Merge branch 'dev' into command_example_usage 21 Nov. 2018 J-Donald Tournier 0074bc6cd15 M Merge pull request #1490 from MRtrix3/connectome_tool_opacity
mrview Connectome tool: 'transparency' -> 'opacity' 21 Nov. 2018 Robert Smith d6f79706532 mrview Connectome tool: 'transparency' -> 'opacity'
Since these capabilities interpret low values as transparent and high values as opaque, 'opacity' is a more appropriate term. It is also more consistent with other mrview tools. 18 Nov. 2018 Thijs Dhollander 1aee9555803 A few example usage changes.
Mostly for dwi2fod, to stick with the basics. More complicated usages, if our pipelines require them, are also documented in those pipelines (and in context). I'd like to keep this basic, so as to not give some users the impression they're running other kinds of algorithms. 21 Nov. 2018 Robert Smith 68b0efb9275 Additional example usages for commands documentation 17 Nov. 2018 Robert Smith 66ce0773c6d mrtrix3.app.Parser.addExampleUsage(): New function
Echoing the changes made in the C++ library in 0344cc65, this function allows the addition of example usages of an executable command to the help page and online documentation. 16 Nov. 2018 Robert Smith db3daedc683 Example usages for more commands 16 Nov. 2018 Robert Smith 0344cc65ec4 New variable MR::App::EXAMPLES
This class allows a command author to insert one or more demonstrative examples of use of the command into the command's help page and online documentation.
It currently only applies to C++ binaries, but an equivalent functionality for Python is expected in the future.
Examples for a limited set of commands that regularly cause user confusion have been added. 16 Nov. 2018 Robert Smith 98ecafbbfdd M Merge pull request #1429 from MRtrix3/amp2response_invalid_transform
amp2response: Exception on invalid transform 15 Nov. 2018 Robert Smith c6105b3a504 M Merge branch 'dev' into amp2response_invalid_transform 15 Nov. 2018 J-Donald Tournier f757c3fa304 M Merge pull request #1483 from MRtrix3/mrcalc_pi
mrcalc: added 'pi' as special keyword. 14 Nov. 2018 Max Pietsch b82003e55f5 mrcalc: docs update 10 Nov. 2018 maxpietsch 32e98642d9a M Merge branch 'dev' into mrcalc_pi 10 Nov. 2018 Max Pietsch a9b7f9a592c mrcalc and math.h: added euler constant. 10 Nov. 2018 Max Pietsch 84f194281cb mrcalc: added 'pi' as special keyword. 10 Nov. 2018 Thijs Dhollander 41941d3db05 M Merge branch 'dev' into amp2response_invalid_transform 09 Nov. 2018 Thijs Dhollander 1b7e61f7ae7 M Merge pull request #1482 from MRtrix3/fix_mrview_norealign_option
Update dev with master hot-fixes 09 Nov. 2018 Thijs Dhollander a7d00062577 M Merge branch 'dev' into fix_mrview_norealign_option 09 Nov. 2018 maxpietsch e6cd0704151 M Merge pull request #1460 from MRtrix3/mrdegibbs_pronoun
mrdegibbs: disambiguate pronoun 02 Oct. 2018 Max Pietsch 224a92e423f mrdegibbs docs update 01 Oct. 2018 Max Pietsch b8c0da6386c Revert "doc update"
This reverts commit c41514f32e48e026bb8cd3ce837a3df94ff76774. 01 Oct. 2018 Max Pietsch c41514f32e4 doc update 30 Sep. 2018 maxpietsch db046afc6c7 mrdegibbs disambiguate pronoun
http://community.mrtrix.org/t/mrtrix-tutorial-available-on-osf/1942/3 30 Sep. 2018 Robert Smith c610f5077ef M Merge pull request #1459 from MPIB/fix_fsl_autodetect
Change FSL autodetect behaviour 24 Sep. 2018 Michael Krause 83ac12a1c66 Change FSL autodetect behaviour
In environments where multiple FSL versions can be loaded (e.g. HPC)
preferring the fsl5.0-X defaults leads to undesirable behaviour.
Users may explicitly activate some custom FSL either with environment
modules or manually with the default FSL setup procedure. If there is
a fsl package installed which prefixes their scripts with "fsl5.0-"
(i.e. neurodebian) mrtrix should not prefer that one over the explicit
user choice. 17 Sep. 2018 Daan Christiaens ead04e72775 M Merge pull request #1456 from MRtrix3/bugfix_4dnodeimage
tck2connectome empty output on 4-D parcellation image 12 Sep. 2018 Robert Smith d313e59758e tck2connectome: Better fix for 4D input images
- In tck2connectome, call MR::Connectome::check() to perform a more comprehensive check of the input parcellation image.
- In MR::Connectome::check(), also check the dimensionality of the input image.
Alternative solution to that contrinuted in e3982a44.
Fixes #1456. 11 Sep. 2018 Daan Christiaens e3982a44800 tck2connectome: check that node input image is 3-D. 10 Sep. 2018 Thijs Dhollander 85f032f0a10 M Merge pull request #1444 from MRtrix3/dwi2fod_produce_modelled_signal
dwi2fod MSMT CSD: option to write predicted signal 30 Aug. 2018 Thijs Dhollander a3891362924 dwi2fod userdocs update 30 Aug. 2018 Max Pietsch ebbabc8d12b M Merge branch 'dev' into dwi2fod_produce_modelled_signal 29 Aug. 2018 J-Donald Tournier 34d4d407071 M Merge pull request #1430 from MRtrix3/command_history_noquotes
command_history: Only use quotes when needed 28 Aug. 2018 Robert Smith 74885866c1f M Merge branch 'dev' into command_history_noquotes 28 Aug. 2018 Robert Smith 1416042addf M Merge pull request #1440 from MRtrix3/tckgen_allow_no_downsampling
tckgen: Permit -downsample 1 24 Aug. 2018 Robert Smith 9414003c628 tckgen: Permit -downsample 1
This is an entirely valid use case to disable downsampling for iFOD2, which unlike other algorithms has downsampling enabled by default. 24 Aug. 2018 Robert Smith 2b2da82938e Header::create(): Remove unused variable 28 Aug. 2018 J-Donald Tournier 1030e519e29 cosmetic fix trigger CI 22 Aug. 2018 J-Donald Tournier 5d0e0f37a93 cosmetic fix 22 Aug. 2018 J-Donald Tournier d2fb0b02f14 M Merge branch 'dev' into command_history_noquotes 22 Aug. 2018 J-Donald Tournier 89f24a9bc9b M Merge pull request #1434 from MRtrix3/handle_dicom_variable_scaling
Handle dicom variable scaling 22 Aug. 2018 J-Donald Tournier 19e1955b6fb M Merge branch 'dev' into handle_dicom_variable_scaling 22 Aug. 2018 Robert Smith 55d10898d15 M Merge pull request #1435 from MRtrix3/silence_compiler_warnings_take3
Silence compiler warnings take3 21 Aug. 2018 Robert Smith 8212598b53d Cleanup of diff for #1435
Commit 11d16a31 reverts changes that were made as part of #1412 to alter the suppression of compiler warnings from non-MRtrix3 source files, as a different solution is provided in 9499316d. However due to the direct use of revert in git, extraneous whitespaces that had been automatically removed by a text editor as part of the changes in #1412 are being re-introduced. This commit simply prevents the re-addition of those whitespaces in order to provide a clean diff f... 21 Aug. 2018 J-Donald Tournier 9499316d771 configure: use -idirafter rather than -isystem
This should avoid issues such as #1390 19 Aug. 2018 J-Donald Tournier 11d16a31b1f Partial revert of pull request #1412 (build tweaks)
This reverts the following commits to restore the -I => -isystem
translation in configure:
* 8431efcdf - TravisCI: Add -Wno-deprecated-register (3 weeks ago) <Robert Smith>
* bf3353cf8 - travis.yml: add -Wno-inconsistent-missing-override to clang/linux test (3 weeks ago) <J-Donald Tournier>
* 2be2eb1ec - add more pragmas to deal with unknown warnings... (3 weeks ago) <J-Donald Tournier>
* f6fb0cec1 - add missing files from previous commit ... 19 Aug. 2018 J-Donald Tournier a4134de741a DICOM: add ImageIO handler for variable scaling 19 Aug. 2018 J-Donald Tournier a984d281c5f add Datatype::is_byte_order_native() call 19 Aug. 2018 Robert Smith 44aa26961ea M Merge pull request #1426 from MRtrix3/mrconvert_update_doc
mrconvert update doc 16 Aug. 2018 Robert Smith c3e0e684612 mrconvert: Remove double-space from help page 16 Aug. 2018 J-Donald Tournier e0ac7f40e96 mrconvert: update help page with reference to number sequences 14 Aug. 2018 ← Prev Next → [{"id": "2d1c38518e687aca6016bef05bbb507a3e1f66cb", "href": "/projects/CONSULT/repos/mrtrix3/commits/2d1c38518e687aca6016bef05bbb507a3e1f66cb","parents": [{ "id": "1aee9555803198489e84ee50a48e8d7a46fc247d" },{ "id": "0074bc6cd153f2f6c8043a36bf5b64dab42a52ab" }]},{"id": "0074bc6cd153f2f6c8043a36bf5b64dab42a52ab", "href": "/projects/CONSULT/repos/mrtrix3/commits/0074bc6cd153f2f6c8043a36bf5b64dab42a52ab","parents": [{ "id": "98ecafbbfdddb30e2702d65242a7fe3c12d4483a" },{ "id": "d6f79706532f1ea4e749ad9479283d6e222efabe" }]},{"id": "d6f79706532f1ea4e749ad9479283d6e222efabe", "href": "/projects/CONSULT/repos/mrtrix3/commits/d6f79706532f1ea4e749ad9479283d6e222efabe","parents": [{ "id": "98ecafbbfdddb30e2702d65242a7fe3c12d4483a" }]},{"id": 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