| 58e9c12 | Michiel Cottaar | 18 May 2020, 13:56:22 UTC | BUG: create scores_str to pass on to python script | 29 June 2020, 12:38:22 UTC |
| c31c72b | Michiel Cottaar | 07 May 2020, 09:06:19 UTC | DOC: better document new code | 29 June 2020, 12:38:22 UTC |
| 60783b7 | Michiel Cottaar | 05 May 2020, 15:28:24 UTC | ENH: optionally run under the old code | 29 June 2020, 12:38:22 UTC |
| 398c520 | Michiel Cottaar | 10 April 2020, 14:51:14 UTC | Recompute average b0 with only undistored b0's Done by iterating the averaging and scoring 3 times | 29 June 2020, 12:38:22 UTC |
| fcdef02 | Michiel Cottaar | 14 February 2020, 14:57:34 UTC | Remove unnecessary echo statement | 29 June 2020, 12:38:22 UTC |
| e683117 | Michiel Cottaar | 14 February 2020, 14:21:16 UTC | BUG: adjust fwhm defaults in parent script as well | 29 June 2020, 12:38:22 UTC |
| bc70083 | Michiel Cottaar | 10 February 2020, 13:21:24 UTC | Actually generate bvals_noRot and bvecs_noRot | 29 June 2020, 12:38:22 UTC |
| 6848d4f | Michiel Cottaar | 06 February 2020, 16:42:39 UTC | Added niter flag and changes the default to 7 (also --fwhm default changed) required to converge when first b0 is very misaligned with the second | 29 June 2020, 12:38:22 UTC |
| 312e7aa | Michiel Cottaar | 06 February 2020, 16:40:10 UTC | Use spaces when pasting bvals/bvecs together for consistency | 29 June 2020, 12:38:22 UTC |
| b124910 | Michiel Cottaar | 06 February 2020, 13:25:13 UTC | Fix data concatenation to take into account extra volume | 29 June 2020, 12:38:22 UTC |
| 8caa0a3 | Michiel Cottaar | 03 February 2020, 11:33:35 UTC | BUG: fix eddy input files | 29 June 2020, 12:38:22 UTC |
| d319389 | Michiel Cottaar | 26 January 2020, 18:20:22 UTC | downsample when determining best B0 | 29 June 2020, 12:38:22 UTC |
| 3d931ba | Michiel Cottaar | 26 January 2020, 18:19:20 UTC | many bug fixes | 29 June 2020, 12:38:22 UTC |
| 7f3695a | Michiel Cottaar | 24 January 2020, 13:42:10 UTC | Only use topups if less than 5 b0's for that phase encoding | 29 June 2020, 12:38:22 UTC |
| ffb08d8 | Michiel Cottaar | 24 January 2020, 13:27:17 UTC | remove duplicate code | 29 June 2020, 12:38:22 UTC |
| b1b8881 | Michiel Cottaar | 24 January 2020, 13:21:42 UTC | many bug fixes | 29 June 2020, 12:38:22 UTC |
| 093662b | Michiel Cottaar | 15 January 2020, 14:17:48 UTC | ENH: don't use topup when there are enough b0's | 29 June 2020, 12:38:22 UTC |
| 580d5f1 | Michiel Cottaar | 13 January 2020, 10:48:18 UTC | various bug fixes | 29 June 2020, 12:38:22 UTC |
| daed9f8 | Michiel Cottaar | 06 January 2020, 17:02:16 UTC | ENH: include positive B0 reference volume as first volume in eddy | 29 June 2020, 12:38:22 UTC |
| 277ab02 | Michiel Cottaar | 06 January 2020, 16:46:50 UTC | ENH: extract best B0 for Pos and Neg | 29 June 2020, 12:38:22 UTC |
| f3823e5 | Michiel Cottaar | 13 November 2019, 14:35:44 UTC | ENH: Score each b0 | 29 June 2020, 12:38:22 UTC |
| 65b0e1f | Aleksij Kraljic | 16 June 2020, 13:15:32 UTC | finalized PhilipsFieldMapPreprocessingAll | 16 June 2020, 13:15:32 UTC |
| b6d7138 | Michael Harms | 22 May 2020, 23:40:25 UTC | Bring the '_1res' script into alignment | 22 May 2020, 23:40:25 UTC |
| 64971e3 | Michael Harms | 22 May 2020, 23:37:19 UTC | Change order of columns in stats file, and change order of code to match, to make it easier to link code together | 22 May 2020, 23:37:19 UTC |
| f4afdc5 | Michael Harms | 22 May 2020, 23:27:24 UTC | Bug: Fix two incorrect column header names in stats file that quantifies overlap between subject ROIs and Atlas | 22 May 2020, 23:27:24 UTC |
| a817acb | Tim Coalson | 27 April 2020, 20:38:34 UTC | Fix error message, some indentation consistency | 27 April 2020, 20:38:34 UTC |
| 5033f4f | Tim Coalson | 13 April 2020, 19:45:05 UTC | comment on remaining fov mask differences | 22 April 2020, 00:08:49 UTC |
| 8f784f3 | Tim Coalson | 10 April 2020, 22:13:15 UTC | add missing "source" line | 22 April 2020, 00:08:49 UTC |
| 4232b2d | Tim Coalson | 10 April 2020, 21:38:38 UTC | address PR comments | 22 April 2020, 00:08:49 UTC |
| 6a40f49 | Tim Coalson | 08 April 2020, 02:11:25 UTC | initial code for wb_command resampling of timeseries to replace slow fslsplit/convertwarp/applywarp/fslmerge code | 22 April 2020, 00:08:49 UTC |
| 10e1818 | Aleksij | 10 April 2020, 06:58:32 UTC | implemented fieldmap distortion correction for Philips scanners | 10 April 2020, 06:58:32 UTC |
| 6f3b402 | Matt Glasser | 06 April 2020, 22:47:31 UTC | Change Large File Deletes Keep unmasked spatially corrected data and delete gdc and mc large timeseries data. | 08 April 2020, 20:27:25 UTC |
| 60cd1d3 | Tim Coalson | 02 April 2020, 20:03:10 UTC | fix typo in SetUp | 02 April 2020, 20:03:10 UTC |
| 939eda7 | Tim Coalson | 02 April 2020, 01:51:12 UTC | Update version.txt | 02 April 2020, 01:51:12 UTC |
| a4728cc | Matt Glasser | 02 April 2020, 00:59:52 UTC | Address Tim Concerns | 02 April 2020, 01:18:20 UTC |
| 31ea9a0 | Matt Glasser | 02 April 2020, 00:02:23 UTC | Enable Single Regression in RSNRegression Enable a new 'single' mode of temporal regression for RSNRegression to enable applying existing results to a new CIFTI space or single regression in other contexts | 02 April 2020, 01:18:20 UTC |
| d78b33a | Tim Coalson | 20 March 2020, 18:43:44 UTC | update version.txt | 20 March 2020, 18:43:44 UTC |
| 49830a6 | Michael Hodge | 16 March 2020, 21:29:12 UTC | MATLAB compile: functionhighpassandvariancenormalize | 17 March 2020, 08:26:30 UTC |
| b140561 | Michael Harms | 16 March 2020, 15:59:26 UTC | Add reporting of percentage of masked voxels | 17 March 2020, 08:26:30 UTC |
| 38d0aa0 | Michael Harms | 12 March 2020, 21:18:13 UTC | Fix some whitespace (tab vs space) misalignment | 17 March 2020, 08:26:30 UTC |
| 787dbfc | Michael Harms | 12 March 2020, 20:15:57 UTC | Delete 'data' once done with it | 17 March 2020, 08:26:30 UTC |
| bbc3ba5 | Michael Harms | 12 March 2020, 19:58:06 UTC | Decrease memory usage of icaDim by using 'range' instead of 'std'; Add Tim's modifications to not mask if it isn't actually helpful | 17 March 2020, 08:26:30 UTC |
| 4f912a4 | Michael Harms | 12 March 2020, 19:45:57 UTC | Decrease memory usage of functionhighpass by using 'range' instead of 'std' to compute mask | 17 March 2020, 08:26:30 UTC |
| 756d25a | Michael Harms | 11 March 2020, 22:29:23 UTC | Some minor code restructuring to hopefully faciliate readability | 17 March 2020, 08:26:30 UTC |
| a460a35 | Matt Glasser | 11 March 2020, 00:55:13 UTC | Update icaDim.m Break up expressions | 17 March 2020, 08:26:30 UTC |
| 7a2ad58 | Matt Glasser | 10 March 2020, 23:50:55 UTC | Update icaDim.m Down to 3 copies. | 17 March 2020, 08:26:30 UTC |
| ef87528 | Matt Glasser | 10 March 2020, 23:07:29 UTC | Update icaDim.m Try again now with max 4 copies. | 17 March 2020, 08:26:30 UTC |
| b20239b | Matt Glasser | 10 March 2020, 21:14:59 UTC | Update icaDim.m Reduce Memory Usage of icaDim | 17 March 2020, 08:26:30 UTC |
| 4251ee4 | Michael Hodge | 09 March 2020, 19:57:23 UTC | MATLAB compile: functionhighpassandvariancenormalize | 17 March 2020, 08:26:30 UTC |
| 6063323 | Michael Harms | 05 March 2020, 19:13:25 UTC | Add a couple linebreaks just to match other code | 17 March 2020, 08:26:30 UTC |
| 3f9af1c | Tim Coalson | 04 March 2020, 22:17:10 UTC | change single(zeros(... to zeros(..., 'single') | 17 March 2020, 08:26:30 UTC |
| d55ad14 | Tim Coalson | 04 March 2020, 20:53:38 UTC | Change shell rm to matlab delete | 17 March 2020, 08:26:30 UTC |
| 35845d3 | Michael Harms | 04 March 2020, 17:21:59 UTC | Forgot to modify the fslmaths -bptf call to operate on the original fmri file as input | 17 March 2020, 08:26:30 UTC |
| 8fb53a7 | Michael Harms | 04 March 2020, 17:01:23 UTC | More logical and efficient sequence of steps for the the hp>0 condition | 17 March 2020, 08:26:30 UTC |
| c42c7ae | Matt Glasser | 03 March 2020, 22:06:46 UTC | Reduce volume memory usage Reduce memory usage when computing variance normalization on volume files. | 17 March 2020, 08:26:30 UTC |
| 987ea31 | Tim Coalson | 03 March 2020, 22:14:56 UTC | add nfs temporaries to gitignore | 03 March 2020, 22:14:56 UTC |
| dcd48ac | Michael Harms | 28 February 2020, 23:26:13 UTC | Fix small bug in usage statement | 28 February 2020, 23:26:13 UTC |
| 8d867a1 | Michael Harms | 28 February 2020, 16:56:20 UTC | Update 1res script to match as regards the reporting on the subcortical segmentation | 28 February 2020, 16:56:20 UTC |
| 31c1952 | Michael Harms | 19 February 2020, 18:34:26 UTC | Keep the dilated version of the brainmask | 27 February 2020, 20:36:49 UTC |
| 0027037 | Michael Harms | 18 February 2020, 16:46:09 UTC | Add some subcortical missing/overlap counts after applying dilation, so as to discount for voxels near the borders | 27 February 2020, 20:36:49 UTC |
| 1a44c6d | Michael Harms | 12 February 2020, 19:19:31 UTC | Extend the checking of the subcortical segmentation to report separately for each structure, and include additional info regarding overlap with the Atlas | 27 February 2020, 20:36:49 UTC |
| 25475f8 | Michael Harms | 24 February 2020, 19:54:36 UTC | Bug fix to cleaned movement regressor code, plus minor simplification | 27 February 2020, 18:34:47 UTC |
| bb1bfe0 | Michael Harms | 20 February 2020, 17:59:40 UTC | Move out-of-place log messages related to 'melodic' to just prior to actually running 'melodic' | 20 February 2020, 17:59:40 UTC |
| 9e03f31 | Matt Glasser | 14 February 2020, 21:23:04 UTC | Update hcp_fix_multi_run Address Mike and Tim's concerns | 19 February 2020, 21:04:43 UTC |
| 033271c | Matt Glasser | 11 February 2020, 16:19:49 UTC | Enable Creation of Cleaned Movement Regressors Regress sICA noise components out of movement regressors to enable their use on sICA+FIX cleaned fMRI data. The files are present in text and .nii.gz formats and for both the concatinated and single runs | 19 February 2020, 21:04:43 UTC |
| 6fef275 | Tim Coalson | 12 February 2020, 19:14:49 UTC | update version.txt | 12 February 2020, 19:14:49 UTC |
| 3771742 | Tim Coalson | 24 January 2020, 22:26:32 UTC | update version.txt | 24 January 2020, 22:26:32 UTC |
| 70171d2 | glasserm | 24 January 2020, 21:54:24 UTC | Address Mike's comments and multiple grayordinates resolutions Address Mike's comments and make sure this works in the case of multiple grayordinates resolutions. | 24 January 2020, 22:24:43 UTC |
| 5530df3 | glasserm | 23 January 2020, 23:42:14 UTC | Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh Address Tim comments | 24 January 2020, 22:24:43 UTC |
| 570c2d2 | glasserm | 23 January 2020, 23:25:38 UTC | Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh Add column for brainstem specifically | 24 January 2020, 22:24:43 UTC |
| 89916a6 | glasserm | 23 January 2020, 22:48:59 UTC | Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh Address Mike Harms comments | 24 January 2020, 22:24:43 UTC |
| a0ee1c8 | glasserm | 23 January 2020, 20:00:48 UTC | Update FreeSurfer2CaretConvertAndRegisterNonlinear.sh Add checking for mismatching atlas subcortical segmentation and subject's brain mask | 24 January 2020, 22:24:43 UTC |
| a194c89 | Tim Coalson | 23 January 2020, 21:27:58 UTC | As wb >=1.4.0 cifti resample outputs exact zeros past the dilation edge, use a separate dilation step for speed | 23 January 2020, 21:27:58 UTC |
| 351f7b4 | glasserm | 22 January 2020, 23:28:23 UTC | Update SubcorticalProcessing.sh Increase dilation to avoid invalid CIFTI files being produced. | 22 January 2020, 23:28:23 UTC |
| c9a821d | glasserm | 22 January 2020, 23:11:23 UTC | Revert "add a dilation step after subcortical resampling to prevent all-zero subcortical grayordinates" This reverts commit bcdf5f624255bf34d86158a4a2d5c5198ef26300. | 22 January 2020, 23:11:23 UTC |
| bcdf5f6 | Tim Coalson | 22 January 2020, 00:18:12 UTC | add a dilation step after subcortical resampling to prevent all-zero subcortical grayordinates | 22 January 2020, 00:18:12 UTC |
| 3b5daee | Tim Coalson | 08 January 2020, 22:47:07 UTC | fix duplicate names in our freesurfer LUTs (and sort by key) | 08 January 2020, 22:47:07 UTC |
| f652296 | Tim Coalson | 06 January 2020, 20:11:09 UTC | update version.txt | 06 January 2020, 20:11:09 UTC |
| 3e1356e | Tim Coalson | 06 January 2020, 20:10:47 UTC | update version.txt | 06 January 2020, 20:10:47 UTC |
| bbcff01 | Michael Harms | 30 December 2019, 16:05:27 UTC | Bug: Fix missing space in 'if' conditional' | 30 December 2019, 16:05:27 UTC |
| 0fc2672 | Tim Coalson | 26 December 2019, 22:36:28 UTC | update version.txt | 26 December 2019, 22:36:28 UTC |
| 8a1bc30 | Tim Coalson | 26 December 2019, 22:36:01 UTC | update version.txt | 26 December 2019, 22:36:01 UTC |
| 2549018 | Michael Harms | 23 December 2019, 21:40:08 UTC | Bug fix to CreateDenseTimeseries when we don't have full grayordinate coverage | 23 December 2019, 21:40:08 UTC |
| 4f55045 | Michael Harms | 17 December 2019, 21:08:35 UTC | Fix bug in reporting version of mri_surf2surf | 17 December 2019, 21:08:35 UTC |
| 872e116 | Tim Coalson | 10 December 2019, 19:42:16 UTC | update version.txt | 10 December 2019, 19:42:16 UTC |
| 5ede0aa | Tim Coalson | 10 December 2019, 19:39:32 UTC | update version.txt | 10 December 2019, 19:39:32 UTC |
| c3fc0ea | Michael Harms | 27 November 2019, 21:24:03 UTC | Update DistortionCorrection Usage statement to match style of GenericfMRIVolume; Allow --usejacobian to have any case | 27 November 2019, 23:27:02 UTC |
| 606d7ff | Michael Harms | 27 November 2019, 19:42:19 UTC | Some minor tweaks and typo corrections to the --processing-mode-info statement | 27 November 2019, 23:27:02 UTC |
| cf7c89f | Michael Harms | 27 November 2019, 19:01:27 UTC | BUG: Fix 'if' syntax in new opts_CheckForFlag function | 27 November 2019, 23:27:02 UTC |
| 3860b34 | Grega Repovs | 27 November 2019, 16:07:26 UTC | Added processing mode information and a function for checking of existence of a specific flag | 27 November 2019, 23:27:02 UTC |
| 0a07ac9 | Michael Harms | 26 November 2019, 20:50:40 UTC | Change from '--boldmask' to '--fmrimask', and rename internal variable accordingly | 27 November 2019, 23:27:02 UTC |
| 805d850 | Michael Harms | 26 November 2019, 19:59:37 UTC | Tweaks to Usage statement; generally replace 'BOLD' with 'fMRI' | 27 November 2019, 23:27:02 UTC |
| f6e8eb2 | Grega Repovs | 26 November 2019, 12:44:59 UTC | Added initial description of legacy mode processing parameters for fMRIVolume pipeline. | 27 November 2019, 23:27:02 UTC |
| 4880ba8 | Michael Harms | 25 November 2019, 23:09:07 UTC | Use quotation marks consistently in Usage statement | 27 November 2019, 23:27:02 UTC |
| 26df033 | Michael Harms | 25 November 2019, 23:02:11 UTC | Add Abort if other required parameters are not specified | 27 November 2019, 23:27:02 UTC |
| 5d30ec2 | Michael Harms | 25 November 2019, 22:52:54 UTC | Add compliance checking of SDC related inputs | 27 November 2019, 23:27:02 UTC |
| 00feef3 | Michael Harms | 25 November 2019, 20:53:59 UTC | Return to GDC having no default | 27 November 2019, 23:27:02 UTC |
| 9b5f6d0 | Michael Harms | 25 November 2019, 17:26:19 UTC | Usage statement tweaks; Set GDC to 'NONE' as default; Log MotionCorrectionType | 27 November 2019, 23:27:02 UTC |
| 125387f | Michael Harms | 22 November 2019, 23:23:23 UTC | Add Usage statement to fMRIVolume | 27 November 2019, 23:27:02 UTC |
| 6fbfd51 | Michael Harms | 22 November 2019, 21:12:57 UTC | Add a simple Usage statement to fMRISurface | 27 November 2019, 23:27:02 UTC |
