| 1334b35 | Daisuke MATSUYOSHI | 02 October 2020, 04:04:54 UTC | Fixed variable name typo Fixed typo and made a variable name consistent between VolumeProcessingPipelineBatch and SurfaceProcessingPipelineBatch | 16 February 2021, 01:12:52 UTC |
| 5bcf9f4 | Tim Coalson | 13 February 2021, 02:16:10 UTC | remove version.txt, edit things that used it to use show_version | 16 February 2021, 01:09:46 UTC |
| d37267b | Tim Coalson | 12 February 2021, 00:06:53 UTC | typo in comment | 16 February 2021, 01:09:46 UTC |
| a335c32 | Tim Coalson | 12 February 2021, 00:01:35 UTC | Add explanation, remove unhelpful error, git magic to ignore changes in Examples | 16 February 2021, 01:09:46 UTC |
| 17bd858 | Tim Coalson | 08 February 2021, 21:28:36 UTC | reorder option parsing for consistency | 16 February 2021, 01:09:46 UTC |
| 8fb1980 | Tim Coalson | 08 February 2021, 21:25:12 UTC | rework show_version | 16 February 2021, 01:09:46 UTC |
| 7b9b08c | Tim Coalson | 08 February 2021, 17:08:28 UTC | update version.txt | 08 February 2021, 17:08:28 UTC |
| 716e9f4 | Tim Coalson | 11 January 2021, 22:45:35 UTC | add "set -e" to DeDrift... to handle debug trap not being active inside functions | 11 January 2021, 22:45:35 UTC |
| 63f37cf | Tim Coalson | 08 January 2021, 01:00:37 UTC | indentation cleanup | 11 January 2021, 22:38:59 UTC |
| 109b2b7 | Michael Harms | 06 January 2021, 22:35:32 UTC | Template scene for fMRI QC | 11 January 2021, 22:38:59 UTC |
| 08a32b3 | Michael Harms | 06 January 2021, 21:56:54 UTC | Logging tweaks; harmonize logging of structural and fMRI QC | 11 January 2021, 22:38:59 UTC |
| 1a26e4b | Michael Harms | 06 January 2021, 21:39:07 UTC | Fix bug due to repeated path info | 11 January 2021, 22:38:59 UTC |
| 8a6d319 | Michael Harms | 06 January 2021, 19:17:13 UTC | fMRI QC generation needs to occur at end of fMRISurface, rather than fMRIVolume | 11 January 2021, 22:38:59 UTC |
| 9aac688 | Michael Harms | 06 January 2021, 18:27:00 UTC | Fix bug in scene capture | 11 January 2021, 22:38:59 UTC |
| 68e3d17 | Michael Harms | 06 January 2021, 17:30:24 UTC | Fix bug in call to GenerateFMRIScenes.sh | 11 January 2021, 22:38:59 UTC |
| a0ab845 | Michael Harms | 04 January 2021, 22:52:51 UTC | Update dummy variable strings to match those used in template. | 11 January 2021, 22:38:59 UTC |
| adb35d9 | Michael Harms | 23 December 2020, 23:42:07 UTC | Add quotation marks for whitespace protection | 11 January 2021, 22:38:59 UTC |
| de3c6b9 | Michael Harms | 23 December 2020, 23:38:23 UTC | Switch from 'notmasked' to 'nomask' as suffix | 11 January 2021, 22:38:59 UTC |
| c2cd99a | Michael Harms | 23 December 2020, 21:04:03 UTC | Add fmri-qc option and associated handling to fMRIVolume | 11 January 2021, 22:38:59 UTC |
| 2c6bb1e | Michael Harms | 23 December 2020, 19:57:23 UTC | First pass at fMRI QC scene generation script | 11 January 2021, 22:38:59 UTC |
| bcd3c39 | Michael Harms | 23 December 2020, 19:21:10 UTC | OutputSceneFolder is already an absolute path | 11 January 2021, 22:38:59 UTC |
| babf803 | Michael Harms | 23 December 2020, 19:16:48 UTC | Remove unnecessary variable. | 11 January 2021, 22:38:59 UTC |
| e95f8f2 | Michael Harms | 23 December 2020, 18:42:03 UTC | Separate relativePath function into own library | 11 January 2021, 22:38:59 UTC |
| d14c4b2 | Michael Harms | 22 December 2020, 19:41:45 UTC | Generate Atlas_mean.dscalar.nii ni CreateDenseTimeseries, for display by fMRIQC. | 11 January 2021, 22:38:59 UTC |
| 5cad816 | Michael Harms | 22 December 2020, 19:16:34 UTC | Generate bias corrected and intensity normalized, but unmasked version of Scout. | 11 January 2021, 22:38:59 UTC |
| 3440b2c | Tim Coalson | 23 December 2020, 21:44:31 UTC | update version.txt | 23 December 2020, 21:44:31 UTC |
| 61c94a0 | Tim Coalson | 03 December 2020, 21:54:39 UTC | explanation and error checking in tempfiles | 03 December 2020, 21:54:39 UTC |
| dd0522e | Tim Coalson | 03 December 2020, 02:49:08 UTC | mask out some background noise to reduce file size | 03 December 2020, 21:48:09 UTC |
| e81e154 | Tim Coalson | 03 December 2020, 00:19:11 UTC | move QC templates folder, delete unused and redundant files, replace regex find with something simple | 03 December 2020, 21:48:09 UTC |
| e1d5839 | Tim Coalson | 01 December 2020, 00:27:01 UTC | update batch example for PostFS | 03 December 2020, 21:48:09 UTC |
| 88e58e8 | Tim Coalson | 30 November 2020, 23:55:27 UTC | StructuralQC integration | 03 December 2020, 21:48:09 UTC |
| eef67b9 | Michiel Cottaar | 02 December 2020, 17:06:14 UTC | BUG: allow for partial acquisition of a session | 03 December 2020, 13:54:27 UTC |
| e2d5004 | Michiel Cottaar | 02 December 2020, 13:13:32 UTC | Support CombineDataFlag of 0 when averaging rotated bvecs | 03 December 2020, 13:54:27 UTC |
| eb9ac23 | Michael Harms | 01 December 2020, 17:57:41 UTC | Add missing redirect symbol Co-authored-by: Michiel Cottaar <MichielCottaar@protonmail.ch> | 03 December 2020, 13:54:27 UTC |
| 2dd1c1e | Michael Harms | 20 November 2020, 20:36:06 UTC | Fix bug on when bvecs_noRot is created | 03 December 2020, 13:54:27 UTC |
| 4672d9d | Michael Harms | 20 November 2020, 19:37:23 UTC | Add more explanatory comments | 03 December 2020, 13:54:27 UTC |
| 07f01a3 | Michael Harms | 20 November 2020, 18:47:20 UTC | Move code for better symmetry across conditionals | 03 December 2020, 13:54:27 UTC |
| 893e155 | Michael Harms | 20 November 2020, 18:34:23 UTC | Fix creation of bvecs_noRot in one of the conditionals | 03 December 2020, 13:54:27 UTC |
| e2d5bba | Tim Coalson | 30 November 2020, 23:43:31 UTC | change 91282 template to cifti-2 format, minor edits to newopts | 30 November 2020, 23:43:31 UTC |
| e0d895e | Michiel Cottaar | 26 October 2020, 15:33:01 UTC | BUG: fixes b-value & gradient orientation for the selected b0 | 26 October 2020, 15:33:01 UTC |
| cd8f164 | Tim Coalson | 08 September 2020, 21:53:50 UTC | Merge pull request #194 from mindbrainlab/unified_fieldmap Unified fieldmap | 08 September 2020, 21:53:50 UTC |
| 226a958 | Tim Coalson | 08 September 2020, 21:53:05 UTC | update version.txt | 08 September 2020, 21:53:05 UTC |
| 0c5f317 | Aleksij | 01 September 2020, 20:12:52 UTC | merged master into unified_fieldmaps and resolved conflicts | 01 September 2020, 20:12:52 UTC |
| cdd3b76 | Aleksij | 28 August 2020, 08:39:39 UTC | Added image demeaning to avoid voxel translation | 28 August 2020, 08:39:39 UTC |
| 9d8e5ae | Aleksij | 27 August 2020, 08:59:57 UTC | fix: included echodiff parameter for Philips fieldmap distortion correction | 27 August 2020, 08:59:57 UTC |
| 0e56b9b | Aleksij | 27 August 2020, 07:39:18 UTC | redesigned Philip B0 map correction as the code for Siemens scanners | 27 August 2020, 07:39:18 UTC |
| 6c33037 | Tim Coalson | 25 August 2020, 20:29:16 UTC | update version.txt | 25 August 2020, 20:29:16 UTC |
| cdc0733 | Michiel Cottaar | 25 August 2020, 19:40:22 UTC | Removed comments put in for testing | 25 August 2020, 20:18:38 UTC |
| 03a59a5 | Michiel Cottaar | 25 August 2020, 08:54:47 UTC | Don't skip printing input variables | 25 August 2020, 20:18:38 UTC |
| b4c5937 | Michiel Cottaar | 24 August 2020, 11:28:09 UTC | add flags to correct commad line | 25 August 2020, 20:18:38 UTC |
| 82b1a49 | Michiel Cottaar | 24 August 2020, 11:11:14 UTC | pass on --no-gpu and --cuda--version | 25 August 2020, 20:18:38 UTC |
| e999db5 | Michiel Cottaar | 24 August 2020, 11:05:13 UTC | fix mixing of tabs and spaces | 25 August 2020, 20:18:38 UTC |
| ed26c33 | Michael Harms | 24 August 2020, 22:31:12 UTC | Fix file comparison to work with error trapping | 24 August 2020, 22:44:40 UTC |
| 74618e8 | Michael Harms | 21 August 2020, 23:32:30 UTC | Remove hard-coded setting of --flm=quadratic, since that is already the default in 'eddy' | 24 August 2020, 22:44:40 UTC |
| b70606f | Michael Harms | 21 August 2020, 23:31:14 UTC | Detect whether 'std' and 'gpuEnabled' eddy are the same | 24 August 2020, 22:44:40 UTC |
| 2fd800b | Michael Harms | 21 August 2020, 23:04:01 UTC | Reverse order of checking for eddy_cuda vs. eddy | 24 August 2020, 22:44:40 UTC |
| b19b047 | Tim Coalson | 21 August 2020, 19:52:06 UTC | fix overlooked mktemp | 21 August 2020, 19:52:06 UTC |
| c467404 | Aleksij | 18 August 2020, 09:13:51 UTC | minor format changes to fieldmap preprocessing script | 20 August 2020, 14:27:55 UTC |
| dd77430 | Aleksij | 07 August 2020, 10:40:27 UTC | Combined all three (Siemens/Philips/GeneralElectric) fieldmap distortion correction scripts into a single script. | 20 August 2020, 14:27:55 UTC |
| 8e136fd | Aleksij Kraljic | 16 June 2020, 13:15:32 UTC | finalized PhilipsFieldMapPreprocessingAll | 20 August 2020, 14:27:55 UTC |
| b1ebe19 | Aleksij | 10 April 2020, 06:58:32 UTC | implemented fieldmap distortion correction for Philips scanners | 20 August 2020, 14:27:55 UTC |
| c1c40c8 | Aleksij | 18 August 2020, 09:13:51 UTC | minor format changes to fieldmap preprocessing script | 18 August 2020, 09:13:51 UTC |
| 93c8372 | Aleksij | 07 August 2020, 10:40:27 UTC | Combined all three (Siemens/Philips/GeneralElectric) fieldmap distortion correction scripts into a single script. | 07 August 2020, 10:40:27 UTC |
| 6db0210 | Tim Coalson | 31 July 2020, 05:47:42 UTC | bugfix: missing run handling in Extract... | 31 July 2020, 05:47:42 UTC |
| f2eeef9 | Tim Coalson | 27 July 2020, 20:55:52 UTC | update comment about clean_vn files | 27 July 2020, 22:14:43 UTC |
| 590d566 | Tim Coalson | 25 July 2020, 00:15:23 UTC | update comment about copying clean_vn files | 27 July 2020, 22:14:43 UTC |
| fff985e | Tim Coalson | 24 July 2020, 01:31:41 UTC | help info and naming, make --concat-reg-name require --dedrift-reg-files | 27 July 2020, 22:14:43 UTC |
| c37eacc | Tim Coalson | 22 July 2020, 01:36:31 UTC | accept MSMSulc in Extract script | 27 July 2020, 22:14:43 UTC |
| 75f0715 | Tim Coalson | 21 July 2020, 23:06:27 UTC | mharms comments, help info | 27 July 2020, 22:14:43 UTC |
| cb658d6 | Tim Coalson | 21 July 2020, 00:10:16 UTC | options for DeDrift to generate additional MR FIX extracted files, some whitespace editing | 27 July 2020, 22:14:43 UTC |
| 9eb6e1c | Tim Coalson | 16 July 2020, 18:07:00 UTC | use registration name or volume files when getting run lengths | 27 July 2020, 22:14:43 UTC |
| 301b603 | Tim Coalson | 08 July 2020, 01:57:11 UTC | fix errors found in testing, expand help info | 27 July 2020, 22:14:43 UTC |
| d04d5a4 | Tim Coalson | 07 July 2020, 01:52:36 UTC | first attempt, untested | 27 July 2020, 22:14:43 UTC |
| 884e27c | Grega Repovs | 21 July 2020, 13:11:47 UTC | Merge branch 'master' into philips_fieldmap | 21 July 2020, 13:11:47 UTC |
| 703543e | glasserm | 08 July 2020, 00:07:42 UTC | *Fix Motion Correction Mask Spam #183 Because this uses an already working construct, testing is not needed. | 08 July 2020, 00:07:42 UTC |
| 510fcfd | Tim Coalson | 29 June 2020, 22:27:56 UTC | update version.txt | 29 June 2020, 22:27:56 UTC |
| 6980bc6 | Michiel Cottaar | 24 June 2020, 09:20:11 UTC | We also don't need spaced here when using log_Warn | 29 June 2020, 12:38:22 UTC |
| ed6c3e3 | Michiel Cottaar | 24 June 2020, 09:19:04 UTC | Removed spaces that are no longer needed | 29 June 2020, 12:38:22 UTC |
| f37c978 | Michiel Cottaar | 23 June 2020, 08:21:10 UTC | Addressed remaining of @mharms commments | 29 June 2020, 12:38:22 UTC |
| cb39341 | Michiel Cottaar | 23 June 2020, 08:18:54 UTC | Fix usage of awk | 29 June 2020, 12:38:22 UTC |
| 4cddb1f | Michiel Cottaar | 23 June 2020, 08:16:24 UTC | Apply suggestions from code review Co-authored-by: Michael Harms <mharms@wustl.edu> | 29 June 2020, 12:38:22 UTC |
| f344e28 | Michiel Cottaar | 20 June 2020, 11:12:12 UTC | Removed fsl_sub again | 29 June 2020, 12:38:22 UTC |
| ee09424 | Michiel Cottaar | 20 June 2020, 10:56:43 UTC | Support b0maxbval in basic_preproc_best_b0.sh script | 29 June 2020, 12:38:22 UTC |
| c252d87 | Michiel Cottaar | 20 June 2020, 09:44:21 UTC | Clarify first volume will be removed again | 29 June 2020, 12:38:22 UTC |
| 864a546 | Michiel Cottaar | 20 June 2020, 09:42:06 UTC | Fixed typo | 29 June 2020, 12:38:22 UTC |
| e182e72 | Michiel Cottaar | 20 June 2020, 09:36:14 UTC | Log message indicating what is being run | 29 June 2020, 12:38:22 UTC |
| 07b0ef8 | Michiel Cottaar | 19 June 2020, 16:32:42 UTC | Raise error of --dont_peas and --select_best_b0 flags are both set | 29 June 2020, 12:38:22 UTC |
| 41b4313 | Michiel Cottaar | 19 June 2020, 11:24:23 UTC | Massive reformatting of the code using pycharm's "reformat code" option I mostly ran this to fix the indentation (which after my editing was inconsistent between two spaces or tabs; should be tabs everywhere now) Pycharm did also fix some other issues: - got rid of some excess spaces - Replaced old `COMMAND` with $(COMMAND) - ensured while COND ; do and if COND ; then are on one line I also added quotes around $@ to prevent resplitting of arguments as they get passed along | 29 June 2020, 12:38:22 UTC |
| dccad75 | Michiel Cottaar | 19 June 2020, 11:04:00 UTC | Many other updates suggested by @mharms | 29 June 2020, 12:38:22 UTC |
| 8a7022a | Michiel Cottaar | 19 June 2020, 10:42:17 UTC | Don't produce bvals_noRot | 29 June 2020, 12:38:22 UTC |
| 2d58d9b | Michiel Cottaar | 19 June 2020, 10:02:00 UTC | Use log_warn and explain warning better | 29 June 2020, 12:38:22 UTC |
| 6cf92b3 | Michiel Cottaar | 19 June 2020, 09:40:51 UTC | Add actual b-value and gradient orientation of best b0 | 29 June 2020, 12:38:22 UTC |
| b7df44b | Michiel Cottaar | 19 June 2020, 09:23:04 UTC | Be more precise in which bvals/bvecs should be merged | 29 June 2020, 12:38:22 UTC |
| d31d723 | Michiel Cottaar | 19 June 2020, 09:18:47 UTC | Added comments explaining general approach | 29 June 2020, 12:38:22 UTC |
| 4c855a4 | Michiel Cottaar | 19 June 2020, 09:09:15 UTC | Don't pass on unused b0dist and b0maxbval to basic_preproc_best_b0.sh | 29 June 2020, 12:38:22 UTC |
| 010d304 | Michiel Cottaar | 19 June 2020, 08:57:12 UTC | BUG: remove fsl_sub | 29 June 2020, 12:38:22 UTC |
| bdf6505 | Michiel Cottaar | 19 May 2020, 08:49:57 UTC | BUG: correct usage of -z query in bash | 29 June 2020, 12:38:22 UTC |
| 557a239 | Michiel Cottaar | 18 May 2020, 20:47:55 UTC | Print warning message if not increasing FWHM when running --select-best-b0 | 29 June 2020, 12:38:22 UTC |
| f219e5d | Michiel Cottaar | 18 May 2020, 20:40:25 UTC | Revert to default niter value of 5 (set by eddy) | 29 June 2020, 12:38:22 UTC |
| 54fa3ff | Michiel Cottaar | 18 May 2020, 20:36:24 UTC | Revert to default --fwhm=0 | 29 June 2020, 12:38:22 UTC |
