Author Commit Message Commit Date Lee Reid 943dfdba150 M Merge branch 'tckgen_init_direction_image' into dev 20 Feb. 2020 Lee Reid 7b197999655 small change to allow building on older g++ versions 20 Feb. 2020 Lee Reid 5c0a57aa95c M Merge remote-tracking branch 'github/dev' into dev 01 Apr. 2019 Robert Smith d605171cc25 M Merge pull request #1566 from EmilieMcKinnon/read_write_tsf_matlab
read and write tsf .m files 21 Feb. 2019 Emilie McKinnon a9c9a703a96 tsf .m files
wrote .m files to read and write .tsf files in matlab 14 Feb. 2019 Robert Smith 1f59b7f1ac1 M Merge pull request #1556 from MRtrix3/tck_duplicate_roi_fix
Prevent duplicated ROI entries in track files 09 Feb. 2019 Robert Smith 817d8cb3c18 M Merge branch 'dev' into tck_duplicate_roi_fix 08 Feb. 2019 Robert Smith 2cb3dabb7fb M Merge pull request #1547 from MRtrix3/tcksift2_linear_option
tcksift2: Add -linear option 07 Feb. 2019 Robert Smith 5532ae957a1 M Merge branch 'dev' into tcksift2_linear_option 07 Feb. 2019 Robert Smith 3aa77de5bbc M Merge pull request #1554 from MRtrix3/deep_multithreading
Prevent deep multi-threading 07 Feb. 2019 Robert Smith 5d9be7ce063 Prevent deep multi-threading
If the static multi-threading backend class already exists when some piece of code queries the number of threads available, then some higher-level functionality is already operating in a multi-threaded fashion, and therefore instruct that code to run single-threaded instead. 07 Feb. 2019 Robert Smith 37694a5a625 Docs: Remove erroneously-inserted script from list 04 Feb. 2019 Robert Smith 1bdf4265a6a tcksift2 -linear: Fix for non-contributing streamlines 01 Nov. 2017 Robert Smith d7b21627827 tcksift2: New option -linear
The code for this feature was added a long time ago, but command-line access to the functionality was never provided.
When using the -linear option, the command estimates a weighting factor for each streamline in a single step, with each factor determined independently. This is a considerably different approach to the primary SIFT2 optimisation algorithm, but nevertheless operates on a similar principle, and with the same fundamental goal. Its main use is in the ... 26 Oct. 2017 J-Donald Tournier 9497a1d9fe7 tckedit: use C++11 range-based for loops where possible 08 Feb. 2019 Robert Smith 44a028d5658 Prevent duplicated ROI entries in track files
Issue was due to parsing of ROIs from command-line being shifted into Tractography::load_rois() function in 965db317, but not being correspondingly removed from Tracking::load_streamline_properties(). 07 Feb. 2019 Robert Smith 18965e6beb0 M Merge pull request #1489 from MRtrix3/command_example_usage
Command example usages in documentation 14 Jan. 2019 Robert Smith 36a2d2929b2 M Merge branch 'dev' into command_example_usage 14 Jan. 2019 Robert Smith ca806b049ec M Merge pull request #1534 from MRtrix3/dwiintensitynorm_fix
dwiintensitynorm: Fix bug introduced in #1389 14 Jan. 2019 Robert Smith 01b1ea4beb6 M Merge branch 'dev' into dwiintensitynorm_fix 14 Jan. 2019 Robert Smith 16dcf6af9c9 M Merge pull request #1535 from MRtrix3/travisci_macosx_qt
TravisCI: Try to fix Qt installation 14 Jan. 2019 Robert Smith 84d757359ed TravisCI: Explicit brew update call on OSX 14 Jan. 2019 Robert Smith b1691f715af TravisCI: Try adding envvars for macosx 14 Jan. 2019 Robert Smith 97ea2c305fa TravisCI: Try to fix Qt installation 14 Jan. 2019 Robert Smith d679eee159a dwiintensitynorm: Fix bug introduced in #1389
Function app.mrconvertOutputOption() can only be applied when run.command() is calling mrconvert; the command-line options it exploits are not present in other binaries. 13 Jan. 2019 Max Pietsch 7c00c1535f2 rerun travis 12 Jan. 2019 Robert Smith 63b7afcabc2 M Merge branch 'dev' into command_example_usage 10 Jan. 2019 Robert Smith 614e82fd47f M Merge pull request #1529 from MRtrix3/5ttgen_5ttcheck_fix
5ttgen: 5ttcheck fix 09 Jan. 2019 Robert Smith 46d1db4db4d 5ttgen: Fix erroneous warning
In 63f51aad, the 5ttcheck command was altered to print a console message if all input images check out OK. This however conflicts with the 5ttgen script, which used non-empty 5ttcheck stderr contents to trigger a warning message. This commit alters 5ttgen to examine the 5ttcheck output contents more closely, only echoing any warnings if any were actually issued. 09 Jan. 2019 Robert Smith 9ecff16c897 M Merge pull request #1512 from MRtrix3/hotfix_to_dev
Hotfix to dev 12 Dec. 2018 Robert Smith 4fe7438fddf M Merge branch 'master' into hotfix_to_dev
Conflicts:
lib/mrtrix3/_5ttgen/gif.py 12 Dec. 2018 Robert Smith ae63c77becb M Merge pull request #1511 from MRtrix3/fsl_eddybinary_mac_fix
dwipreproc: Search PATH for 'eddy_cpu' 12 Dec. 2018 Robert Smith d9a9123370c M Merge branch 'master' into fsl_eddybinary_mac_fix 12 Dec. 2018 Robert Smith d7f497c910f M Merge pull request #1510 from MRtrix3/tckstats_explicit_fix
Explicit streamline length calculation on master 12 Dec. 2018 Robert Smith f3ba5569c4a M Merge branch 'master' into tckstats_explicit_fix 12 Dec. 2018 Robert Smith e890d83626a M Merge pull request #1509 from MRtrix3/dwipreproc_fsl6_volcombine_fix
dwipreproc: Compatibility with FSL6.0.0 12 Dec. 2018 J-Donald Tournier d2c27797ae1 TravisCI: try using git repo to fetch Eigen 12 Dec. 2018 Robert Smith 1c0a046af58 dwipreproc: Compatibility with FSL6.0.0
In this particular version of FSL, the image output by the --fout option of the topup command generates a 4D image, where the first volume is the expected field map image, but the other volumes are intensity-scaled versions of the uncorrected input images. While this is certainly an FSL bug, the dwipreproc script nevertheless needs to be compatible with such data. Currently it causes an issue only when explicit DWI volume recombination is to be perform... 08 Dec. 2018 Robert Smith bbfdaeaa247 Streamline::calc_length(): Make no assumptions
Previous version of this function estimated the step size from the central segment of the streamline, and then assumed that this step size applied to the rest of the streamline (apart from the first and last segments) by calling the Streamline::calc_length(float step_size) function. If streamlines have been non-linearly warped, this is not going to be a safe assumption. Therefore, both in any context where a fixed step size is not known, or in t... 09 Dec. 2018 Robert Smith 52d80fa68e1 dwipreproc: Search PATH for 'eddy_cpu' 09 Dec. 2018 Thijs Dhollander 9c3de06d643 M Merge pull request #1499 from MRtrix3/dicom_fix_slice_timing_mismatch_in_mosaic
DICOM: be more lenient with slice timing vector in Siemens mosaics 27 Nov. 2018 Thijs Dhollander 95facfc3489 M Merge branch 'master' into dicom_fix_slice_timing_mismatch_in_mosaic 27 Nov. 2018 Thijs Dhollander 9ed5c9f6bb2 M Merge pull request #1498 from MRtrix3/mrview_screen_capture_translate_camera_fix
MRView: fix translation in camera coordinates in screen capture tool 27 Nov. 2018 Robert Smith 48d013c24b9 M Merge branch 'master' into mrview_screen_capture_translate_camera_fix 27 Nov. 2018 Robert Smith a93b4320b6c M Merge pull request #1504 from MRtrix3/python_image_statistic_fix
mrtrix3.image.statistic(): Fix parameter naming 27 Nov. 2018 Robert Smith 2e0a7f52216 _5ttgen/gif.py: Remove extraneous pylint directive 27 Nov. 2018 J-Donald Tournier 5f57d8fd86d 5ttgen GIF algorithm: fix for pylint errors 26 Nov. 2018 J-Donald Tournier db10b20b366 run_pylint: fix to report correct version information 26 Nov. 2018 J-Donald Tournier a045b9206f4 run_pylint: log version information for potential debugging 26 Nov. 2018 J-Donald Tournier 6605eb4c5ed M Merge branch 'master' into python_image_statistic_fix 26 Nov. 2018 Next → [{"id": "943dfdba150bcb25d90f28d7c42b69c5f49701aa", "href": "/projects/CONSULT/repos/mrtrix3/commits/943dfdba150bcb25d90f28d7c42b69c5f49701aa","labels": [{"name": "dev", "type": "BRANCH", "href": "/projects/CONSULT/repos/mrtrix3/browse?at=dev"}],"parents": [{ "id": "5c0a57aa95cc79ac58e791408a97be6e54f7b4c1" },{ "id": "7b1979996558f7a69d2f987446bef403c03ac7ff" }]},{"id": "7b1979996558f7a69d2f987446bef403c03ac7ff", "href": 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