| 600ddc9 | Lennart Verhagen | 15 March 2017, 09:36:38 UTC | Merge branch 'Washington-University/master' | 15 March 2017, 09:36:38 UTC |
| ae69b9a | Matt Glasser | 13 March 2017, 22:20:44 UTC | *Fix not ending function definition in MSMAll/scripts/SingleSubjectConcat.sh | 13 March 2017, 22:25:40 UTC |
| e5377e9 | Timothy B. Brown | 13 March 2017, 22:15:31 UTC | Fixed problem with curly bracket matching in SingleSubjectConcat.sh | 13 March 2017, 22:15:31 UTC |
| 4a44e10 | Matt Glasser | 13 March 2017, 22:05:52 UTC | *Bugfix in MSM command call | 13 March 2017, 22:06:28 UTC |
| c412a99 | Timothy B. Brown | 13 March 2017, 19:59:16 UTC | Merging | 13 March 2017, 19:59:16 UTC |
| 074631f | Matt Glasser | 12 March 2017, 20:31:33 UTC | *Commit deletes | 13 March 2017, 19:56:07 UTC |
| 91d4a70 | Matt Glasser | 12 March 2017, 20:25:25 UTC | *Modify MSMAll Pipeline to not depend on the RestingStateStats Pipeline: *Also fix bugs related to running MSMAll with newer versions of the minimal preprocessing pipelines *MSMAll now has a new required argument --high-pass=<high-pass filter used in ICA+FIX> *matlab function ssConcat is removed and ComputeVN is added | 13 March 2017, 19:55:52 UTC |
| d2e2fce | Timothy B. Brown | 13 March 2017, 16:49:33 UTC | Merging Matt's changes so that MSMAll Pipeline does not depend on RestingStateStats Pipeline | 13 March 2017, 19:47:17 UTC |
| b76b673 | Matt Glasser | 12 March 2017, 20:31:33 UTC | *Commit deletes | 12 March 2017, 20:31:33 UTC |
| 0084ca9 | Matt Glasser | 12 March 2017, 20:25:25 UTC | *Modify MSMAll Pipeline to not depend on the RestingStateStats Pipeline: *Also fix bugs related to running MSMAll with newer versions of the minimal preprocessing pipelines *MSMAll now has a new required argument --high-pass=<high-pass filter used in ICA+FIX> *matlab function ssConcat is removed and ComputeVN is added | 12 March 2017, 20:25:25 UTC |
| c74ad21 | Lennart Verhagen | 09 March 2017, 16:38:52 UTC | Merge branch 'Washington-University/master' | 09 March 2017, 16:38:52 UTC |
| 962f018 | Timothy B. Brown | 07 March 2017, 16:52:58 UTC | Working on preparing code for using different versions of MATLAB. | 07 March 2017, 16:52:58 UTC |
| af90660 | Matt Glasser | 06 March 2017, 16:00:46 UTC | *Add in new template for MSMSulc | 06 March 2017, 16:01:42 UTC |
| e126c69 | Timothy B. Brown | 18 February 2017, 02:09:53 UTC | Created Version v3.22.0-beta.5 | 18 February 2017, 02:09:53 UTC |
| 8fbeb26 | Timothy B. Brown | 17 February 2017, 20:51:15 UTC | Created Version v3.22.0-beta.4 | 17 February 2017, 20:51:15 UTC |
| e95edc6 | Timothy B. Brown | 17 February 2017, 19:01:51 UTC | Working on getting ReApplyFixPipeline.sh to work for hand reclassified HCP 3T Subjects | 17 February 2017, 19:01:51 UTC |
| 58781fb | Timothy B. Brown | 16 February 2017, 17:01:35 UTC | Created Version v3.22.0-beta.3 | 16 February 2017, 17:01:35 UTC |
| d409b02 | Timothy B. Brown | 14 February 2017, 22:40:36 UTC | Recompiled a version of fix_3_clean.m | 14 February 2017, 22:40:36 UTC |
| 0beeec1 | Timothy B. Brown | 14 February 2017, 22:27:16 UTC | Working on getting ReApplyFix to work for subjects that have hand reclassifications | 14 February 2017, 22:27:16 UTC |
| 1bf5b14 | Timothy B. Brown | 10 February 2017, 18:06:32 UTC | Moving example batch script for ApplyHandReClassifications pipeline to Examples/Scripts directory | 10 February 2017, 18:06:32 UTC |
| ede1a9e | Timothy B. Brown | 10 February 2017, 18:03:03 UTC | Added debugging/logging completion notification to end of MergeEditClassifications MATLAB function | 10 February 2017, 18:03:03 UTC |
| 037699a | Timothy B. Brown | 10 February 2017, 17:51:23 UTC | Corrected the function declaration in MergeEditClassifications MATLAB code to work in compiled MATLAB mode | 10 February 2017, 17:51:23 UTC |
| d18e17e | Timothy B. Brown | 10 February 2017, 17:23:54 UTC | First compiled version of the MergeEditClassifications MATLAB code in ApplyHandReClassifications pipeline | 10 February 2017, 17:23:54 UTC |
| fe13e3b | Timothy B. Brown | 10 February 2017, 16:17:31 UTC | Working on ApplyHandReClassifications pipeline. Ready to compile Matlab code. | 10 February 2017, 16:17:31 UTC |
| fdc8eaf | Timothy B. Brown | 09 February 2017, 22:09:33 UTC | Merge remote-tracking branch 'origin/master' | 09 February 2017, 22:09:33 UTC |
| f77e698 | Timothy B. Brown | 09 February 2017, 22:08:31 UTC | Early work on ApplyHandReClassifications pipeline | 09 February 2017, 22:08:31 UTC |
| 29eba7d | Lennart Verhagen | 06 February 2017, 21:21:18 UTC | Merge branch 'Washington-University/master' | 06 February 2017, 21:21:18 UTC |
| 93865ad | Matt Glasser | 31 January 2017, 01:19:26 UTC | *Resolve GitHub Issue #30 | 31 January 2017, 01:19:26 UTC |
| ad56ff5 | Matt Glasser | 24 January 2017, 01:59:04 UTC | *Add reclean after hand classification option to ReApplyFIX Pipeline *UNTESTED* | 24 January 2017, 01:59:04 UTC |
| 7a0bbd9 | Timothy B. Brown | 20 January 2017, 19:07:53 UTC | Created Version v3.22.0-beta.2 | 20 January 2017, 19:07:53 UTC |
| 4b87532 | Timothy B. Brown | 20 January 2017, 15:56:17 UTC | Changed toolboxes on path setting for compiled matlab projects | 20 January 2017, 15:56:17 UTC |
| 78e22ea | Timothy B. Brown | 20 January 2017, 15:23:44 UTC | Marking development after v3.22.0.beta-1 | 20 January 2017, 15:23:44 UTC |
| 903e836 | Timothy B. Brown | 19 January 2017, 21:20:48 UTC | Created Version v3.22.0-beta.1 | 19 January 2017, 21:20:48 UTC |
| 17c0f08 | Matt Glasser | 19 January 2017, 12:46:58 UTC | *Fix some bugs in MSMSulc part of PostFreeSurfer | 19 January 2017, 12:46:58 UTC |
| 6b840b7 | Matt Glasser | 16 January 2017, 16:52:16 UTC | *PostFIX edits to enable working with FIXMultiRun | 16 January 2017, 16:54:12 UTC |
| b7bcfdf | Matt Glasser | 16 January 2017, 16:51:00 UTC | *Add MSMSulc (currently untested) and some other minor changes | 16 January 2017, 16:54:12 UTC |
| 9bdb175 | Timothy B. Brown | 12 January 2017, 22:53:03 UTC | Got all Matlab code to compile under Matlab R2013a on my workstation | 12 January 2017, 22:53:03 UTC |
| ec57ef7 | Timothy B. Brown | 12 January 2017, 21:00:18 UTC | Added gifti-1.5 in global/matlab space for Matlab compiles | 12 January 2017, 21:00:18 UTC |
| df9b327 | Matt Glasser | 11 January 2017, 16:49:38 UTC | *Recompiled Matlab binaries for MSMAll and DeDriftAndResample, compiled on Matlab 2016a | 11 January 2017, 16:49:38 UTC |
| 2c8e96c | Matt Glasser | 11 January 2017, 16:42:24 UTC | *Revert paths in setup and batch scripts to defaults | 11 January 2017, 16:42:24 UTC |
| 0f5a5f0 | Matt Glasser | 11 January 2017, 07:51:54 UTC | *Bugfixes for RestingStateStats for bad movement regressors (e.g. column of zeros, non-full-rank matrix) | 11 January 2017, 07:51:54 UTC |
| 5a37db9 | Matt Glasser | 11 January 2017, 07:49:43 UTC | *Same changes for DeDriftAndResamplePipeline and some bug fixes | 11 January 2017, 07:49:43 UTC |
| 365be3e | Matt Glasser | 10 January 2017, 16:58:40 UTC | *Revert Examples/Scripts/SetUpHCPPipeline.sh to prior version | 10 January 2017, 16:58:40 UTC |
| f01b18e | Matt Glasser | 10 January 2017, 16:54:02 UTC | *Get MSMAll Pipeline ready for beta release by adding back in interpreted matlab pathway, updating code to my latest version, making example batch script and adding new configs | 10 January 2017, 16:54:02 UTC |
| b74792a | Timothy B. Brown | 21 December 2016, 17:26:28 UTC | Fixed bug in bedpostx README.md file | 21 December 2016, 17:26:28 UTC |
| d15f885 | Timothy B. Brown | 21 December 2016, 17:24:26 UTC | Added HCP's version of the bedpostx_gpu script | 21 December 2016, 17:24:26 UTC |
| 5c9fe2c | Lennart Verhagen | 09 December 2016, 11:24:25 UTC | Merge branch 'Washington-University/master' | 09 December 2016, 11:24:25 UTC |
| bc9304d | Timothy B. Brown | 02 December 2016, 22:21:08 UTC | Added comment about applicability of section in RestingStateStats.sh that creates sebased bias field. | 02 December 2016, 22:21:08 UTC |
| 7eeee16 | Timothy B. Brown | 02 December 2016, 16:01:51 UTC | Created Version v3.21.0 | 02 December 2016, 16:01:51 UTC |
| b0343c8 | Timothy B. Brown | 01 December 2016, 22:02:34 UTC | Movement of variance normalization file (_vn) in Resting State Stats pipeline is no longer done with mv_if_exists. It is again done with mv, which should correctly signal an error if the file does not exist. | 01 December 2016, 22:02:34 UTC |
| f79cbdb | Timothy B. Brown | 30 November 2016, 22:44:37 UTC | Made RestingStateStats.sh only move certain files if the files actually exist. | 30 November 2016, 22:44:37 UTC |
| 269f1b4 | Timothy B. Brown | 29 November 2016, 18:59:36 UTC | Created Version v3.21.0-alpha.1 | 29 November 2016, 18:59:36 UTC |
| a6b8f3e | Timothy B. Brown | 29 November 2016, 18:56:18 UTC | Changes to run 2mm resolution 7T RestingStateStats | 29 November 2016, 18:56:18 UTC |
| a22a52f | Timothy B. Brown | 18 November 2016, 21:34:14 UTC | Added setting of matlab_compiler_runtime in RestingStateStats based upon CLUSTER environment variable | 18 November 2016, 21:34:14 UTC |
| 5cd7b2d | Timothy B. Brown | 14 November 2016, 15:48:37 UTC | Changed check in comment | 14 November 2016, 15:48:37 UTC |
| ae2ec85 | Timothy B. Brown | 14 November 2016, 15:44:24 UTC | Fixed bug with use of ResultsFolder that I introduced in check in before last. | 14 November 2016, 15:47:07 UTC |
| 6b61f19 | Timothy B. Brown | 14 November 2016, 15:44:24 UTC | Fixed bug with use of I introduced in check in before last. | 14 November 2016, 15:44:24 UTC |
| df6ccf0 | Timothy B. Brown | 11 November 2016, 17:22:07 UTC | Changes to average_bvecs from Stam to handle smaller number of diffusion scans for a subject. | 11 November 2016, 17:22:07 UTC |
| 3e77f9e | Timothy B. Brown | 11 November 2016, 16:13:46 UTC | Added DCFolderName and DCFolder variables in GenericfMRIVolumeProcessingPipeline.sh | 11 November 2016, 16:13:46 UTC |
| a5967d3 | Timothy B. Brown | 10 November 2016, 18:21:35 UTC | Used AtlasSpaceFolder and ResultsFolder variables appropriately in creating final resolution bias field outputs when BiasCorrection is SEBASED | 10 November 2016, 18:21:35 UTC |
| 059e300 | Timothy B. Brown | 27 October 2016, 16:28:16 UTC | Created Version v3.20.0 | 27 October 2016, 16:28:16 UTC |
| 6e22e45 | Timothy B. Brown | 26 October 2016, 21:25:09 UTC | Removed attempted support for a mulit-token value for the --printcom= option in a number of scripts. Enhanced the FSL version check in run_eddy.sh to identify the GPU-enabled and non-GPU-enabled versions of the eddy binary based upon the FSL version in use. Removed fallback to using non-GPU-enabled version of eddy binary when use of GPU-enabled version is requested. Created version v3.20.0-alpha.2 | 26 October 2016, 21:25:09 UTC |
| 8d8aadc | Timothy B. Brown | 25 October 2016, 15:44:37 UTC | Created Version v3.20.0-alpha1 | 25 October 2016, 15:44:37 UTC |
| f77d131 | Timothy B. Brown | 25 October 2016, 15:37:53 UTC | Added movement of eddy log files to package location in PostEddy phase of Diffusion Preprocessing | 25 October 2016, 15:37:53 UTC |
| eb37ba8 | HCP Pipeline Account | 18 October 2016, 21:21:11 UTC | Started development after v3.19.0 | 18 October 2016, 21:21:11 UTC |
| 7dda7e8 | HCP Pipeline Account | 07 October 2016, 17:18:14 UTC | Created Version v3.19.0 | 07 October 2016, 17:18:14 UTC |
| dd770f4 | Timothy B. Brown | 06 October 2016, 19:57:48 UTC | Created Version v3.18.0 | 06 October 2016, 19:57:48 UTC |
| a779fbd | Timothy B. Brown | 06 October 2016, 19:51:21 UTC | Added --with_outliers option to invocation of GPU enabled eddy binary in run_eddy.sh script | 06 October 2016, 19:51:21 UTC |
| 42e80a8 | Timothy B. Brown | 06 October 2016, 15:44:31 UTC | changed --extra-eddy-args= parameter to a repeatable --extra-eddy-arg= parameter | 06 October 2016, 15:44:31 UTC |
| a24be18 | Timothy B. Brown | 05 October 2016, 19:08:08 UTC | Added --extra-eddy-args= parameter to DiffPreprocPipeline.sh. Added/Exposed --combine-data-flag= parameter in DiffPreprocPipeline.sh and DifPreprocPipeline_PostEddy.sh | 05 October 2016, 19:08:08 UTC |
| 4fef378 | Timothy B. Brown | 04 October 2016, 20:28:54 UTC | Merge remote-tracking branch 'origin/master' Merge Diffusion Preprocessing changes with pull requests previously merged by Tim Coalson. | 04 October 2016, 20:28:54 UTC |
| 9af64c7 | Timothy B. Brown | 04 October 2016, 20:24:15 UTC | Changes for latest version of eddy used in Diffusion Preprocessing | 04 October 2016, 20:24:15 UTC |
| cdd9f1d | Tim Coalson | 03 October 2016, 22:31:39 UTC | fix indention in helper function | 03 October 2016, 22:31:39 UTC |
| 79ce5b9 | Chad Donahue | 24 August 2016, 18:01:35 UTC | Fixed bug causing 'no such file' error when using fieldmap distortion correction | 03 October 2016, 22:28:54 UTC |
| 77d8f31 | cjdonahue | 06 June 2016, 18:45:37 UTC | If NHP, use brain-extracted scout for registration to T1w space | 03 October 2016, 22:28:54 UTC |
| e7254f5 | Tim Coalson | 22 September 2016, 21:38:48 UTC | add readme explaining files in standard_mesh_atlases | 22 September 2016, 21:38:48 UTC |
| 7cc0bf1 | Timothy B. Brown | 13 September 2016, 21:29:20 UTC | Added and corrected comments in example batch scripts for DiffusionPreprocessing and for GenericfMRIVolumeProcessing | 13 September 2016, 21:29:20 UTC |
| 9d3c770 | Timothy B. Brown | 01 September 2016, 18:34:20 UTC | Fix example batch scripts so that command line specification of subject list works as an actual list of more than one subject. | 01 September 2016, 18:34:20 UTC |
| 64f6aa7 | Stam Sotiropoulos | 03 August 2016, 14:39:54 UTC | Revise brain_mask to make sure it excludes regions with no diffusion data, but where the mask is non-zero | 03 August 2016, 14:39:54 UTC |
| ab8895f | Tim Coalson | 28 July 2016, 20:07:30 UTC | add files for resampling between fsaverage and fs_LR | 28 July 2016, 20:07:30 UTC |
| 6c20ecc | Lennart Verhagen | 28 June 2016, 09:52:26 UTC | Merge branch 'Washington-University/master' | 28 June 2016, 09:52:26 UTC |
| 65b5aca | Timothy B. Brown | 11 June 2016, 02:25:37 UTC | Created Version v3.17.0 | 11 June 2016, 02:25:37 UTC |
| e8b6829 | Timothy B. Brown | 08 June 2016, 23:10:20 UTC | Added InRegName parameter to DeDriftAndResamplePipeline.sh | 08 June 2016, 23:10:20 UTC |
| 7245620 | Timothy B. Brown | 08 June 2016, 20:16:03 UTC | Added optional Myelin Target File to DeDriftAndResamplePipeline for use in 7T HighRes processing | 08 June 2016, 20:16:03 UTC |
| a1d2ea1 | Timothy B. Brown | 08 June 2016, 19:57:29 UTC | Corrected spelling error in DeDriftAndResamplePipeline.sh | 08 June 2016, 19:57:29 UTC |
| a9aa67a | Timothy B. Brown | 03 June 2016, 15:04:09 UTC | Created Version v3.16.1 | 03 June 2016, 15:04:09 UTC |
| 506df2c | Timothy B. Brown | 03 June 2016, 14:59:35 UTC | created version of hcp_fix for use with FIX 1.06a (separate from version for FIX 1.062). hcp_fix is now a sybolic link to the version intended to be used | 03 June 2016, 14:59:35 UTC |
| d6826c8 | Timothy B. Brown | 03 June 2016, 14:43:51 UTC | Merge remote-tracking branch 'origin/master' | 03 June 2016, 14:43:51 UTC |
| 4195db3 | Timothy B. Brown | 03 June 2016, 14:41:51 UTC | Working on reverting hcp_fix to the fix v1.06a version | 03 June 2016, 14:41:51 UTC |
| d1d800a | Tim Coalson | 02 June 2016, 21:36:50 UTC | fix use of mask in final location before it is copied there | 02 June 2016, 21:36:50 UTC |
| d32be97 | Timothy B. Brown | 02 June 2016, 16:55:12 UTC | Some ICAFIX related changes to improve our custom hcp_fix script and make sure other local changes to FIX scripts are included | 02 June 2016, 16:55:12 UTC |
| 4af2b72 | Timothy B. Brown | 01 June 2016, 20:46:29 UTC | Created branch for 7T DeDriftAndResample changes | 01 June 2016, 20:46:29 UTC |
| 7ee88c0 | Timothy B. Brown | 01 June 2016, 20:18:27 UTC | Created Version v3.16.0 | 01 June 2016, 20:18:27 UTC |
| 34018c2 | Timothy B. Brown | 01 June 2016, 20:13:04 UTC | Merge pull request #22 from Washington-University/inflate_adjust Inflate adjust Pull in Tim Coalson's changes in the inflate_adjust branch to: Use a scaling formula for all inflated surface generation, and add optional extra scaling factor for use on different species. | 01 June 2016, 20:13:04 UTC |
| ee9f21f | Timothy B. Brown | 01 June 2016, 18:30:04 UTC | Merge branch 'ICAFIX_for_7T' | 01 June 2016, 18:30:04 UTC |
| 58b201e | Timothy B. Brown | 01 June 2016, 18:25:48 UTC | Changes to ReApplyFixPipeline.sh to make it work on CHPC 2.0 and get correct FSL version information | 01 June 2016, 18:25:48 UTC |
| 0fdd472 | Timothy B. Brown | 01 June 2016, 18:24:48 UTC | Changes to make PostFix.sh work on CHPC 2.0 | 01 June 2016, 18:24:48 UTC |
| 07c75fc | Timothy B. Brown | 01 June 2016, 18:24:04 UTC | Changes to use version 1.062 of FIX | 01 June 2016, 18:24:04 UTC |
| 18b23c6 | Tim Coalson | 27 May 2016, 02:55:04 UTC | unset POSIXLY_CORRECT in another place, so fsl_sub doesn't break things | 27 May 2016, 02:55:04 UTC |
| 9a34b5d | Tim Coalson | 18 May 2016, 23:29:33 UTC | use scaling formula for all inflated surface generation, add optional extra scaling for use on different species, etc | 18 May 2016, 23:29:33 UTC |
