| 6e2fe5e | Timothy Brown | 21 March 2014, 21:19:28 UTC | Created Version v3.1RC5 | 21 March 2014, 21:19:28 UTC |
| 49de93a | Timothy Brown | 21 March 2014, 21:11:19 UTC | * Changes to handle change in CIFTI file filed name from "TimeStep" to "SeriesStep" * Uses version of wb_command (Workbench command) to support the above field name change * Change output of mcflirt_acc.sh to the mc.par file to allow values to be as wide as necessary and guarantee a single space between each value | 21 March 2014, 21:11:19 UTC |
| 4a1dfa5 | Timothy Brown | 20 March 2014, 15:28:17 UTC | MotionCorrection_FLIRTbased.sh - Added comments mcflirt_acc.sh - Changed output of values to mc.par file to allow values to be as wide as necessary and guarantee a single space between each value | 20 March 2014, 15:28:17 UTC |
| 6ebfd83 | Timothy Brown | 20 March 2014, 14:09:00 UTC | Fix locating PreEddy, Eddy, and PostEddy invocations in DiffPreprocPipeline.sh | 20 March 2014, 14:09:00 UTC |
| 535f429 | Timothy Brown | 19 March 2014, 19:29:34 UTC | Moving NRGDEV testing scripts out of repo | 19 March 2014, 19:29:34 UTC |
| c50129c | Timothy Brown | 19 March 2014, 17:14:05 UTC | Created Version v3.1RC4 | 19 March 2014, 17:14:05 UTC |
| 025be08 | Timothy Brown | 19 March 2014, 17:12:12 UTC | Break DiffPreprocPipeline.sh into 3 stages: PreEddy, Eddy, and PostEddy | 19 March 2014, 17:12:12 UTC |
| 6b4af67 | Timothy Brown | 18 March 2014, 20:21:13 UTC | Break Diffusion Preprocessing into pre-eddy, eddy, and post-eddy | 18 March 2014, 20:21:13 UTC |
| 88a7535 | Timothy Brown | 05 March 2014, 19:01:41 UTC | Created Version v3.1RC3 | 05 March 2014, 19:01:41 UTC |
| 0b6c6e8 | Timothy Brown | 05 March 2014, 18:46:48 UTC | Added code to use GPU-enabled version of FSL eddy program if available. Assumes that the GPU-enabled version of eddy will be named eddy.gpu. Falls back to use the standard version of eddy if eddy.gpu is either not found or returns a failure code. | 05 March 2014, 18:46:48 UTC |
| dcf07aa | Timothy Brown | 28 February 2014, 19:51:16 UTC | Created Version v3.1RC2 | 28 February 2014, 19:51:16 UTC |
| 8984f09 | Timothy Brown | 28 February 2014, 18:07:50 UTC | Created Version v3.1 | 28 February 2014, 18:07:50 UTC |
| 233c712 | Timothy Brown | 28 February 2014, 18:04:40 UTC | Added VersionHistory.md file | 28 February 2014, 18:04:40 UTC |
| a57d1fe | Timothy Brown | 28 February 2014, 17:57:50 UTC | * Included CIFTI-2 version of Workbench command - global/binaries/caret7/exe_rh_linux64/wb_command * Migrate ReadMe from simple text file (ReadMe.txt) to Markdown file (Readme.md) with corresponding generated ReadMe.html | 28 February 2014, 17:57:50 UTC |
| c3d431a | Timothy Brown | 18 February 2014, 17:39:21 UTC | Created Version v3.0 | 18 February 2014, 17:39:21 UTC |
| 0b9896a | Timothy Brown | 11 February 2014, 15:28:10 UTC | Set location of msm binary in NRGDEV version of SetUPHCPPipeline script. Asked msm binary for it's version information before invoking it. | 11 February 2014, 15:28:10 UTC |
| ba9bfa2 | Timothy Brown | 06 February 2014, 16:54:42 UTC | Created Version v3.0RC11 | 06 February 2014, 16:54:42 UTC |
| ba63cec | Timothy Brown | 06 February 2014, 16:53:33 UTC | Revised versions of TaskfMRILevel3.sh and TaskfMRILevel3.bat files to enhance functionality of level 3 analysis. Additional utility script change2unix.pl Changes from Mike Harms and Greg Burgess | 06 February 2014, 16:53:33 UTC |
| 31c5cfc | Timothy Brown | 06 February 2014, 16:39:06 UTC | Added -cortparc3 -parcstats3 flags to final recon-all in FreeSurferPipeline.sh. This computes "extra" cortical parcellation and associated statistics that are available in FreeSurfer v5.3.0 | 06 February 2014, 16:39:06 UTC |
| 0704115 | Timothy Brown | 05 February 2014, 21:51:07 UTC | Created Version v3.0RC10 | 05 February 2014, 21:51:07 UTC |
| 08d8a61 | Timothy Brown | 05 February 2014, 21:48:47 UTC | Zero bound the image and SBRef before normalization. | 05 February 2014, 21:48:47 UTC |
| 229efa8 | Timothy Brown | 05 February 2014, 17:12:58 UTC | Created Version v3.0RC9 | 05 February 2014, 17:12:58 UTC |
| 0061391 | Timothy Brown | 05 February 2014, 16:12:30 UTC | Add copy of final resolution FreeSurfer brain mask to $ResultsFolder | 05 February 2014, 16:12:30 UTC |
| 02ee3b4 | Timothy Brown | 05 February 2014, 16:00:38 UTC | Removed line in OneStepResampling.sh that overwrites binary version of FreeSurfer brain mask with a masked image file. This is so that binary mask can be kept and included in the results. | 05 February 2014, 16:00:38 UTC |
| 87dd258 | Timothy Brown | 05 February 2014, 15:37:50 UTC | TaskfMRILevel1.sh now implements a 2-stage approach to dilating and smoothing. | 05 February 2014, 15:37:50 UTC |
| 37dc08e | Timothy Brown | 05 February 2014, 15:31:03 UTC | Add volume dilation to standard volume-based processing after smoothing. I.e. smooth then dilate. | 05 February 2014, 15:31:03 UTC |
| 38d7113 | Timothy Brown | 05 February 2014, 15:28:36 UTC | Revert TaskfMRILevel1.sh to its state before dilation of BOLD timeseries images. Deciding whether to dilate first then smooth (as the version just prior to this does) or smooth first then dilate. | 05 February 2014, 15:28:36 UTC |
| 33d6d27 | Timothy Brown | 03 February 2014, 17:54:59 UTC | Created Version v3.0RC8 | 03 February 2014, 17:54:59 UTC |
| 40ae299 | Timothy Brown | 03 February 2014, 17:38:22 UTC | Incorporate Mike Harms' suggested comment changes and file naming changes into TaskfMRILevel1.sh. Change formatting some to try to make it easier to read/interpret steps associated with volume dilation. | 03 February 2014, 17:38:22 UTC |
| b1da501 | Timothy Brown | 03 February 2014, 16:44:41 UTC | Removed -fix_mtl from mris_make_surfaces calls | 03 February 2014, 16:44:41 UTC |
| a8d2564 | Timothy Brown | 31 January 2014, 20:52:13 UTC | Mean dilate the volume images using the default kernel just before volume smoothing in Task fMRI analysis, and keep the dilated, un-smoothed versions of these images as part of our intermediate results. | 31 January 2014, 20:52:13 UTC |
| 380b555 | ssothro | 31 January 2014, 12:27:57 UTC | Perform extra dilations to the brain mask before masking the final diffusion data | 31 January 2014, 12:27:57 UTC |
| 6d30bfc | ssothro | 30 January 2014, 10:54:44 UTC | Add a flag to allow greater user flexibility for eddy_combine | 30 January 2014, 10:54:44 UTC |
| b52747a | Timothy Brown | 28 January 2014, 18:38:53 UTC | Created Version v3.0RC7 | 28 January 2014, 18:38:53 UTC |
| 6c8e0a6 | Timothy Brown | 28 January 2014, 18:25:22 UTC | Added -fix_mtl to mris_make_surfaces calls | 28 January 2014, 18:25:22 UTC |
| 7470e8f | Timothy Brown | 27 January 2014, 14:57:00 UTC | Created Version v3.0RC6 | 27 January 2014, 14:57:00 UTC |
| 0753e74 | Timothy Brown | 27 January 2014, 14:55:48 UTC | Fixed bugs - not including function libraries in DiffPreprocPipeline.sh - not using opts_GetOpt1 function in DiffPreprocPipeline.sh | 27 January 2014, 14:55:48 UTC |
| e134b59 | Timothy Brown | 23 January 2014, 22:43:43 UTC | Created Version v3.0RC5 | 23 January 2014, 22:43:43 UTC |
| 268bed2 | Timothy Brown | 23 January 2014, 22:37:14 UTC | Removed the following no longer used custom binaries from the global/binaries directory and adapted scripts to make sure they used the released versions instead of the custom versions * applytopup - code now uses FSL 5.0.6 released version * calc_grad_perc_dev - code now uses FSL 5.0.6 released version * caret5/caret_command - code now uses caret7/wb_command * eddy - code now uses FSL 5.0.6 released version * eddy_combine - code now uses FSL 5.0.6 released version * film_gls - code now uses FSL 5.0.6 released version * topup - code now uses FSL 5.0.6 released version * vecreg - code now uses FSL 5.0.6 released version | 23 January 2014, 22:37:14 UTC |
| 7ff48f6 | Timothy Brown | 22 January 2014, 19:40:24 UTC | Created Version v3.0RC4 | 22 January 2014, 19:40:24 UTC |
| 55a6040 | Timothy Brown | 22 January 2014, 19:35:52 UTC | DiffusionPreprocessing/scripts/run_eddy.sh - no longer uses custom eddy binary. - uses ${FSLDIR}/bin released version of eddy | 22 January 2014, 19:35:52 UTC |
| a08f407 | Timothy Brown | 21 January 2014, 21:01:35 UTC | DiffusionPreprocessing/scripts/eddy_postproc.sh * uses released version of eddy_combine in ${FSLDIR}/bin instead of custom version | 21 January 2014, 21:01:35 UTC |
| 66200c8 | Timothy Brown | 21 January 2014, 20:54:34 UTC | DiffusionPreprocessing/scripts/run_topup.sh * No longer uses custom version of applytopup, uses released version in ${FSLDIR}/bin | 21 January 2014, 20:54:34 UTC |
| c76ac83 | Timothy Brown | 21 January 2014, 20:47:53 UTC | DiffusionPerprocessing/scripts/run_topup.sh * Runs released version of topup in ${FSLDIR}/bin instead of custom topup in ${HCPPIPEDIR_Bin} TaskfMRIAnalysis/TaskfMRIAnalysis.sh * No longer defines or uses GlobalScripts or GlobalBinaries variables TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh * Runs released version of film_gls from ${FSLDIR}/bin instead of film_gls in ${HCPPIPEDIR_Bin} fMRISurface/GenericfMRISurfaceProcessingPipeline.sh * No longer defines or uses GlobalScripts or GlobalBinaries variables fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh * No longer defines or uses GlobalBinaries variable fMRIVolume/scripts/DistoritionCorrectionAndEPIToT1wReg_FLIRTBBRAnd FreeSurferBBRbased.sh * No longer defines or uses GlobalBinaries variable global/scripts/TopupPreprocessingAll.sh * No longer defines or uses GlobalBinaries variable | 21 January 2014, 20:47:53 UTC |
| a1a15a9 | Timothy Brown | 14 January 2014, 20:18:18 UTC | Created Version v3.0RC3 | 14 January 2014, 20:18:18 UTC |
| a8f6467 | Timothy Brown | 10 January 2014, 17:55:11 UTC | Created Version v3.0RC2.3 | 10 January 2014, 17:55:11 UTC |
| 49da59f | Timothy Brown | 10 January 2014, 17:54:09 UTC | Changed format of diffusion data output in DiffPreprocPipeline.sh | 10 January 2014, 17:54:09 UTC |
| d34503a | Timothy Brown | 10 January 2014, 15:24:56 UTC | Created Version v3.0RC2.2 | 10 January 2014, 15:24:56 UTC |
| bbfc08d | Timothy Brown | 03 January 2014, 20:13:45 UTC | Created Version v3.0RC2.1 | 03 January 2014, 20:13:45 UTC |
| b36f3c9 | Timothy Brown | 03 January 2014, 19:37:36 UTC | Merge tag 'v3.0RC2' into 500Subjects HCP Minimal Preprocessing Pipelines V3 Release Candidate 2 | 03 January 2014, 19:37:36 UTC |
| 2887619 | Timothy Brown | 03 January 2014, 19:12:21 UTC | Update version.txt | 03 January 2014, 19:12:21 UTC |
| d93c1d5 | Timothy Brown | 03 January 2014, 19:06:27 UTC | Changed tool and version reporting mechanism | 03 January 2014, 19:06:27 UTC |
| 68df30a | Timothy Brown | 02 January 2014, 19:28:16 UTC | * Changed header commments - Added authors - Removed FreeSurfer Dependency - altered output directories description * Improved/Corrected show_usage function * added logging of platform information via uname -a * removed PipelineScripts and GlobalScripts variables in favor of directly using the HCPPIPEDIR_PreFS and HCPPIPEDIR_Global environment variables | 02 January 2014, 19:28:16 UTC |
| f85c226 | Matt Glasser | 02 January 2014, 18:09:01 UTC | *Improved flat maps (fewer deleted vertices, less distortion) *Set execute bit on FreeSurfer/scripts/FreeSurferHiresPial.sh | 02 January 2014, 18:09:01 UTC |
| c96ffa4 | Timothy Brown | 23 December 2013, 20:39:04 UTC | Added function libraries and logging messages | 23 December 2013, 20:39:04 UTC |
| 545402b | Matt Glasser | 17 December 2013, 06:59:19 UTC | *Improve pial surface performance in FreeSurfer 5.3 | 17 December 2013, 06:59:19 UTC |
| f450fae | Matt Glasser | 17 December 2013, 06:58:35 UTC | *Reduce memory usage of myelin map normalization | 17 December 2013, 06:58:35 UTC |
| 0e15585 | Matt Glasser | 12 December 2013, 00:37:02 UTC | PostFreeSurfer Changes: *Add MSMSulc as an optional registration method. Note that MSM must be installed (not included in the repository) and its path set in the environment variable script Examples/Scripts/SetUpHCPPipeline.sh. Also add FreeSurfer and MSMSulc distortion maps *Add ability to use multiple low resolution meshes and grayordinates voxel spaces (may be needed for 7T processing). These must be defined in advance and put in the templates folders. *Some code cleanup *Fix zeros in the greyordinates space because of bad medial wall definition bug *Add standard flat maps to spec files (if available) *Fix bug where left and right hemisphere FreeSurfer labels were combined in grayordinates space *Optionally allow myelin map bias field correction smoothing to be varied (default is previous hardcoded value) *Fix bug in adaptive barycentric resampling algorithm (i.e. new version of wb_command in previous commit) | 12 December 2013, 00:37:02 UTC |
| a441b04 | Matt Glasser | 12 December 2013, 00:26:20 UTC | fMRIVolume Changes: *Comment cleanup and code cleanup *For GE field map mode (not used by HCP) check that magnitude and T1w brain masks are roughly the same size, if not (i.e. something has gone very wrong) attempt to work around the issue by registering the full brain magnitude image to the T1w and used the structural brain mask on the field map *Detect if processing non-human primate FreeSurfer output and, if so, do extra steps to go between fake 1mm space and subjects native space. This does not affect HCP processing. | 12 December 2013, 00:26:20 UTC |
| 8d85c2e | Matt Glasser | 12 December 2013, 00:20:10 UTC | FreeSurfer Changes: *Comment cleanup *Enable FreeSurfer 5.3 and above -first_wm_peak *Attempt to fix pial surface in FreeSurfer 5.3 (will also benefit 5.2 some) by dilating grey matter normalization out from ribbon | 12 December 2013, 00:20:10 UTC |
| e2ab6d5 | Matt Glasser | 12 December 2013, 00:16:25 UTC | *PreFreeSurfer Changes: *Fix input flag name (s/--echospacing="$TE"/--echodiff="$TE"/g) *Add capability for spin echo field map correction of structural images including necessary additional outputs from TopupPreprocesingAll.sh *Add optional argument to set bias field smoothing (default was previous hard coded setting) *Cosmetic changes to FieldMapPreprocessingAll.sh | 12 December 2013, 00:16:25 UTC |
| 46ce2f9 | Matt Glasser | 11 December 2013, 22:52:12 UTC | *Patch from Keith Jamison (keith.jamison@gmail.com) to fix incorrect half voxel shift in gradient unwarping code | 11 December 2013, 22:52:12 UTC |
| 5624bab | Matt Glasser | 11 December 2013, 22:50:52 UTC | *Use epi_reg from $FSLDIR/bin in diffusion pipeline | 11 December 2013, 22:50:52 UTC |
| 028e0aa | Matt Glasser | 11 December 2013, 22:44:43 UTC | *Update wb_command | 11 December 2013, 22:44:43 UTC |
| 2987e16 | Matt Glasser | 11 December 2013, 22:43:11 UTC | *Clean up unused old files in repo | 11 December 2013, 22:43:11 UTC |
| 24e4f12 | Matt Glasser | 11 December 2013, 22:41:44 UTC | *Modifications (renames, and additions) to global template files | 11 December 2013, 22:41:44 UTC |
| e60eb03 | Matt Glasser | 18 October 2013, 20:47:24 UTC | *Changes to comments in TaskfMRI Pipeline, Add example script for Level3 TaskfMRI script, Clean up unused line in Level3 TaskfMRI script | 18 October 2013, 20:47:24 UTC |
| 28841cd | Matt Glasser | 17 October 2013, 23:21:10 UTC | *Replace film_gls with FSL 5.0.5 version compatible with supercomputer (produces identical results) | 17 October 2013, 23:21:10 UTC |
| 1e60fa1 | Matt Glasser | 04 October 2013, 02:13:22 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 04 October 2013, 02:13:22 UTC |
| 66de9da | Matt Glasser | 04 October 2013, 02:11:56 UTC | *Fix global/scripts/TopupPreprocessingAll.sh for odd numbers of slices (no change to Phase II data processing) | 04 October 2013, 02:11:56 UTC |
| b2103cd | Stam Sotiropoulos | 01 October 2013, 08:52:28 UTC | Small change to PostProcMatrix2 for Mat2 Tractography | 01 October 2013, 08:52:31 UTC |
| 64d97db | Matt Glasser | 30 September 2013, 14:17:28 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 30 September 2013, 14:17:28 UTC |
| e78e806 | Matt Glasser | 30 September 2013, 14:11:40 UTC | *Make DiffPreprocPipeline.sh executable | 30 September 2013, 14:11:40 UTC |
| ade88af | Stam Sotiropoulos | 27 September 2013, 15:02:24 UTC | Tractography Pipelines for Full Dense Connectome Generation | 27 September 2013, 15:02:24 UTC |
| 33d1b63 | Stam Sotiropoulos | 27 September 2013, 11:30:19 UTC | Added DiffusionPreprocessing Example | 27 September 2013, 11:30:19 UTC |
| c58e76c | Matt Glasser | 26 September 2013, 22:12:06 UTC | *Minor updates to PreTractography.sh including example script *Updates to Matt's tractography and post tractography scripts and examples | 26 September 2013, 22:12:06 UTC |
| 23ad6e4 | Stam Sotiropoulos | 29 August 2013, 08:51:24 UTC | Small update... | 29 August 2013, 08:51:24 UTC |
| db8c13b | Stam Sotiropoulos | 29 August 2013, 08:49:44 UTC | Small change in Output directory handling in diffusion pipeline | 29 August 2013, 08:49:47 UTC |
| aea3e21 | Matt Glasser | 22 August 2013, 22:46:13 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 22 August 2013, 22:46:13 UTC |
| 6b95a49 | Matt Glasser | 22 August 2013, 22:32:57 UTC | *Update test for greater compatibility | 22 August 2013, 22:32:57 UTC |
| 8b62f29 | Tony Wilson | 14 August 2013, 15:52:52 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 14 August 2013, 15:52:52 UTC |
| 27a2a97 | Tony Wilson | 14 August 2013, 15:52:22 UTC | made printcom optional | 14 August 2013, 15:52:22 UTC |
| 50b2dd5 | Matt Glasser | 08 August 2013, 23:18:22 UTC | *Update some readmes | 08 August 2013, 23:18:22 UTC |
| 6881302 | Matt Glasser | 05 August 2013, 22:11:33 UTC | *Robustness bugfix to AnatomicalAverage suggested on FSL List | 05 August 2013, 22:11:33 UTC |
| 34dcb3f | Matt Glasser | 31 July 2013, 04:17:39 UTC | *Fix wb_command for cifti to nifti conversion, other fixes and improvements to level 3 task fMRI script. | 31 July 2013, 04:17:39 UTC |
| a9ce427 | Matt Glasser | 26 July 2013, 02:41:40 UTC | *Fix previous commit | 26 July 2013, 02:41:40 UTC |
| 1884291 | Matt Glasser | 26 July 2013, 02:28:34 UTC | *Re-enable custom resolutions for fMRISurface pipeline (no change to ConnectomeDB processing) | 26 July 2013, 02:28:34 UTC |
| fb90ade | Matt Glasser | 25 July 2013, 21:19:06 UTC | *Increase medial wall dilation radius to fix rare taskfMRI pipeline failures | 25 July 2013, 21:19:06 UTC |
| a2b8726 | Matt Glasser | 24 July 2013, 17:29:03 UTC | *Update regular field map fMRIVolume code for FSL 5.0.3 compatibility (no change to ConnectomeDB pipeline process) | 24 July 2013, 17:29:03 UTC |
| a6d1e89 | Matt Glasser | 01 July 2013, 18:32:25 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 01 July 2013, 18:32:25 UTC |
| b52de35 | Matt Glasser | 01 July 2013, 18:30:33 UTC | *Finish Commit for matching fsf files with and without quotes | 01 July 2013, 18:30:33 UTC |
| 5718469 | Tony Wilson | 30 June 2013, 15:18:31 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 30 June 2013, 15:18:31 UTC |
| 7580265 | Matt Glasser | 29 June 2013, 20:17:10 UTC | *Handle inconsistently written npts fsfs | 29 June 2013, 20:17:10 UTC |
| 5ac285d | Matt Glasser | 29 June 2013, 18:35:56 UTC | *Finish previous bugfix commit | 29 June 2013, 18:35:56 UTC |
| 457de66 | Matt Glasser | 29 June 2013, 17:04:26 UTC | *Bugfix for users not using gradient nonlinearity correction with fMRIVolume (not relevant to HCP processing) | 29 June 2013, 17:04:26 UTC |
| b1e9b67 | Tony Wilson | 27 June 2013, 20:02:12 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 27 June 2013, 20:02:12 UTC |
| a87c51d | Matt Glasser | 27 June 2013, 00:03:08 UTC | *Add template dscalar file for 91282 grayordinates | 27 June 2013, 00:03:08 UTC |
| 3e57fc2 | Matt Glasser | 26 June 2013, 18:16:16 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 26 June 2013, 18:16:16 UTC |
| 84c491b | Matt Glasser | 26 June 2013, 17:53:57 UTC | *Fix wb_command for high numbered label keys (fix aparc.a2009s+aseg.nii.gz files from PostFreeSurfer) | 26 June 2013, 17:53:57 UTC |
| d05ab68 | Stam Sotiropoulos | 17 June 2013, 17:31:29 UTC | Minor bug corrections to pretractography scripts | 17 June 2013, 17:34:57 UTC |
