Lee Reid cbab9bbbd42 Copy commit hash iFOD2 was not properly overwriding the truncate method, resulting in rewinding to leave it in the wrong state as this called MethodBase instead 17 Jan. 2018 Lee Reid 745d89aa9fd Copy commit hash retracking now intregrated into exec and works added option to Rewinder to rewind to either the first, middle, or last node within the retrack ROI 16 Jan. 2018 Lee Reid be00cd7c1ca Copy commit hash Added retrack classes, but have not integrated them into exec class Shuffled exec class slightly to behave in a more modular fashion (i.e. make it easier to allow extensions) 16 Jan. 2018 Lee Reid f10973bc9ab Copy commit hash Generated seed_coord option for tckgen, allowing seeding from a specific point 12 Jan. 2018 J-Donald Tournier f098f097ccb M Copy commit hash Merge pull request #1225 from MRtrix3/mrview_black_roi_fix mrview ROI tool: Fix near-black colour selection 02 Jan. 2018 Robert Smith 6a60588fe14 Copy commit hash mrview ROI tool: Fix near-black colour selection Partially addresses #1202. 02 Jan. 2018 Robert Smith 7d68b748b8a M Copy commit hash Merge pull request #1155 from MRtrix3/fsl_checkfirst_function fsl.checkFirst() function 20 Dec. 2017 Thijs Dhollander 5095207f90e M Copy commit hash Merge branch 'master' into fsl_checkfirst_function 19 Dec. 2017 Robert Smith 4fe5e2a1c7f M Copy commit hash Merge pull request #1219 from MRtrix3/5tt2gmwmi_mask_fix 5tt2gmwmi: Fix -mask option 19 Dec. 2017 Thijs Dhollander 597bdcb2be7 M Copy commit hash Merge branch 'master' into fsl_checkfirst_function 19 Dec. 2017 Robert Smith f687d83c60b Copy commit hash labelsgmfix: Remove redundant / erroneous file check 19 Dec. 2017 Robert Smith 9bae6242f17 Copy commit hash 5tt2gmwmi: Fix -mask option Error was made in porting to new syntax as part of 0.3.14, within commit ec49edcaf. 19 Dec. 2017 Robert Smith 6f10915dd43 M Copy commit hash Merge pull request #1168 from MRtrix3/dwigradcheck_fix dwigradcheck: Fix dwi2maskcall 05 Dec. 2017 Robert Smith 505914456d4 M Copy commit hash Merge branch 'master' into dwigradcheck_fix 05 Dec. 2017 J-Donald Tournier d31bb0842a4 M Copy commit hash Merge pull request #1205 from MRtrix3/sh2peaks_fix_z_axis_peaks SH peak finder: fix behaviour at pole for z-aligned delta 01 Dec. 2017 J-Donald Tournier 25cd0e97873 M Copy commit hash Merge branch 'master' into sh2peaks_fix_z_axis_peaks 01 Dec. 2017 J-Donald Tournier 1eba1df8d56 M Copy commit hash Merge pull request #1201 from MRtrix3/population_template_py3_no_numpy_fix population_template: python 3 & no numpy fix 01 Dec. 2017 J-Donald Tournier b498fd373fb Copy commit hash SH peak finder: fix behaviour at pole for z-aligned delta 01 Dec. 2017 J-Donald Tournier f397f99e89a Copy commit hash TravisCI: try using --insecure option to hg to allow mercurial to access the Eigen repo. 01 Dec. 2017 Max Pietsch e2d2755b1c1 Copy commit hash population_template: read and write transformation files in binary 01 Dec. 2017 Max Pietsch 59dac527655 Copy commit hash population template python no numpy: encode string for python 3 compatibility 01 Dec. 2017 Max Pietsch 9a06c28a773 Copy commit hash Revert "population_template: write linear transformation in txt mode, not binary" This reverts commit 068f4bc56f7e4c6fcef521630571d6d9b522518c. 01 Dec. 2017 Max Pietsch 068f4bc56f7 Copy commit hash population_template: write linear transformation in txt mode, not binary 30 Nov. 2017 J-Donald Tournier 21f3d9136c8 M Copy commit hash Merge pull request #1196 from MRtrix3/DICOM_better_handling_of_empty_fields DICOM: fix bug introduced in previous commits 22 Nov. 2017 J-Donald Tournier 195f47708bc M Copy commit hash Merge branch 'master' into DICOM_better_handling_of_empty_fields 22 Nov. 2017 J-Donald Tournier 2cbe4711364 Copy commit hash DICOM: fix bug introduced in previous commits 22 Nov. 2017 J-Donald Tournier d8b9e5e6cf2 M Copy commit hash Merge pull request #1193 from MRtrix3/DICOM_better_handling_of_empty_fields DICOM: better handling of empty fields 21 Nov. 2017 J-Donald Tournier 1251fd679f0 Copy commit hash DICON: read slice position and orientation info from CSA This is required to read Siemens' colFA (DEC) maps correctly. 20 Nov. 2017 J-Donald Tournier bf987a7a495 Copy commit hash DICOM: use %04X tag formatting consistently for debugging output 20 Nov. 2017 J-Donald Tournier 29474b39ba3 Copy commit hash DICOM: fix assert-mode failure 18 Nov. 2017 J-Donald Tournier 115dcf6811e Copy commit hash DICOM: better handling of empty fields 18 Nov. 2017 J-Donald Tournier bb77205ec70 M Copy commit hash Merge pull request #1186 from MRtrix3/fix_help_page_interrupt_handling delay signal handling initialisation 07 Nov. 2017 J-Donald Tournier 5de290e637a Copy commit hash cleanup of signal handling, and delay setting handlers till after cmdline parsing 03 Nov. 2017 J-Donald Tournier b5da4ef22fd M Copy commit hash Merge pull request #1182 from MRtrix3/add_quiet_from_env allow quiet operation from environment variable MRTRIX_QUIET 02 Nov. 2017 Robert Smith 81fd9a2594f M Copy commit hash Merge branch 'master' into add_quiet_from_env 01 Nov. 2017 J-Donald Tournier aa70d1d15e6 Copy commit hash set log_level from MRTRIX_QUIET env variable at initialisation. 01 Nov. 2017 Robert Smith f278f761317 M Copy commit hash Merge pull request #1183 from MRtrix3/spatial_normalisation_typo Typo fix in warping_images_with_warps_from_other_packages 01 Nov. 2017 maxpietsch 144bb5e0966 Copy commit hash Update warping_images_with_warps_from_other_packages.rst 30 Oct. 2017 J-Donald Tournier 7a78a0bc032 Copy commit hash document MRTRIX_QUIET environment variable in -quiet option help string 30 Oct. 2017 J-Donald Tournier b4b30f170ee Copy commit hash allow quiet operation from environment variable MRTRIX_QUIET 27 Oct. 2017 Robert Smith f4d3e52cd81 M Copy commit hash Merge pull request #1179 from MRtrix3/tractography_file_weights_fix Tractography::File::Writer: Fix weights output 26 Oct. 2017 Robert Smith 6317ca374cc M Copy commit hash Merge branch 'master' into tractography_file_weights_fix 26 Oct. 2017 J-Donald Tournier a0ea69952d2 M Copy commit hash Merge pull request #1176 from MRtrix3/fix_mingw_python_path_handling_take2 Ensure the MSY2 version of python is invoked on Windows 26 Oct. 2017 Robert Smith 9bdd0bfc1c8 Copy commit hash Tractography::File::Writer: Fix weights output When creating an output weights file, the App::check_overwrite() function was erroneously being called using the path to the track file rather than the weights file. This would persistently fail, since the header of the track file would be created before the path to the output weights file was specified.
Also cleaned up some connectome2tck code to use smart pointers rather than C-style pointers. 25 Oct. 2017 J-Donald Tournier e835e045fd5 Copy commit hash Better detection of MinGW python This matches if the sys.executable strings starts with a letter followed
by a colon, rather than hardcoding to 'c:/'. 25 Oct. 2017 J-Donald Tournier 1b4b255111c Copy commit hash Ensure the MSY2 version of python is invoked on Windows 24 Oct. 2017 J-Donald Tournier 98a1f83a28d M Copy commit hash Merge pull request #1172 from MRtrix3/fix_set_path_on_windows Fix set_path to look for mrinfo.exe on Windows 24 Oct. 2017 J-Donald Tournier d895347c156 Copy commit hash Fix set_path to look for mrinfo.exe on Windows 20 Oct. 2017 Robert Smith 08994d3e1f7 Copy commit hash dwigradcheck: Fix dwi2maskcall In use case where input image header does not contain a gradient table, and user instead relies on the -grad or -fslgrad option, dwi2mask would fail due to the absence of a gradient table.
Instead have dwi2mask explicitly import from grad.b, which is guaranteed to exist regardless of how the baseline gradient table was provided.
No need to import the gradient table into the image heder for the ... 13 Oct. 2017 Robert Smith 1274689cb42 M Copy commit hash Merge branch 'master' into fsl_checkfirst_function 05 Oct. 2017 
Lee Reid
J-Donald Tournier
Robert Smith
Max Pietsch