| 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 |
| 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 |
| d94334b | Tony Wilson | 11 June 2013, 15:55:37 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 11 June 2013, 15:55:37 UTC |
| db5cc3b | Tony Wilson | 11 June 2013, 15:55:14 UTC | fixed copy/pasta error in TaskfMRIAnalysis | 11 June 2013, 15:55:14 UTC |
| dd7472e | Matt Glasser | 08 June 2013, 19:51:45 UTC | *Fix AtlasRegistrationToMNI152_FLIRTandFNIRT.sh usage formatting (no change to results/calls) | 08 June 2013, 19:51:45 UTC |
| 70c5a39 | Matt Glasser | 04 June 2013, 21:29:06 UTC | *Fix Movement_Regressors.txt by adding a reference volume to the avscale command that decomposes the matrix into translations and rotations *Add Movement_AbsoluteRMS.txt, Movement_RelativeRMS.txt, Movement_AbsoluteRMS_mean.txt, and Movement_RelativeRMS_mean.txt measures of movement | 04 June 2013, 21:29:06 UTC |
| 0630b88 | Matt Glasser | 01 June 2013, 22:44:28 UTC | *PreFreeSurfer bugfix for non-HCP inputs | 01 June 2013, 22:44:28 UTC |
| 5cf27f0 | Matt Glasser | 24 May 2013, 14:26:41 UTC | *Revision of PreTractography scripts *Initial import of Tractography and PostTractography scripts and examples | 24 May 2013, 14:26:41 UTC |
| b9b2574 | Stam Sotiropoulos | 24 May 2013, 10:36:29 UTC | Initial Import of PreTractography scripts | 24 May 2013, 10:36:29 UTC |
| 533b2dc | Stam Sotiropoulos | 24 May 2013, 09:43:41 UTC | Add CARET5DIR global variable | 24 May 2013, 09:43:41 UTC |
| 57e638b | Stam Sotiropoulos | 17 May 2013, 09:42:34 UTC | Add GradientDistortionUnwarp to diffusion pipeline. Make diffusion resolution a parameter to DiffusionToStructural. | 17 May 2013, 09:42:34 UTC |
| 26f2c05 | Stam Sotiropoulos | 13 May 2013, 08:02:58 UTC | Small change to diffusion pipeline | 13 May 2013, 08:02:58 UTC |
| 400bf94 | Stam Sotiropoulos | 10 May 2013, 14:44:22 UTC | Mathcing the diffusion pipeline interface to the other pipelines. Add option for making the grad nonlin correction optional. | 10 May 2013, 14:44:22 UTC |
| b5c3d96 | Matt Glasser | 07 May 2013, 17:51:46 UTC | *Last level 3 task fMRI script bug! | 07 May 2013, 17:51:46 UTC |
| d7c790b | Matt Glasser | 06 May 2013, 21:45:36 UTC | *Bugfix for taskfMRI level 3 (was looking for .func.gii instead of .dtseries.nii) *Cleanup of taskfMRI level 1, 2, and analysis scripts to remove unused code | 06 May 2013, 21:45:36 UTC |
| 31de493 | Matt Glasser | 03 May 2013, 17:37:32 UTC | *Typo bugfix in level 3 task fMRI pipeline | 03 May 2013, 17:37:32 UTC |
| 0ec4ae0 | Matt Glasser | 23 April 2013, 22:23:01 UTC | *Revert change to structural diffusion output folder name | 23 April 2013, 22:23:01 UTC |
| 0576360 | Matt Glasser | 23 April 2013, 22:21:13 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 23 April 2013, 22:21:13 UTC |
| ebdaa60 | Matt Glasser | 23 April 2013, 22:18:29 UTC | *Initial Commit of Task fMRI Analysis Pipeline and Example Script and Data | 23 April 2013, 22:18:29 UTC |
| 73e1899 | Stam Sotiropoulos | 15 April 2013, 12:08:23 UTC | Change Output folder for Diffusion data in T1w space | 15 April 2013, 12:08:23 UTC |
| 9ce3408 | Matt Glasser | 08 April 2013, 01:49:50 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 08 April 2013, 01:49:50 UTC |
| ed989a5 | Matt Glasser | 08 April 2013, 01:49:20 UTC | *Update Readme | 08 April 2013, 01:49:20 UTC |
| 71af01d | Tony Wilson | 02 April 2013, 00:13:32 UTC | changes to recon-all calls | 02 April 2013, 00:13:32 UTC |
| 0871039 | Tony Wilson | 31 March 2013, 16:00:58 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 31 March 2013, 16:00:58 UTC |
| 74450f3 | Matt Glasser | 31 March 2013, 00:38:32 UTC | *Bugfix fMRISurface | 31 March 2013, 00:38:32 UTC |
| dc39323 | Matt Glasser | 30 March 2013, 19:49:10 UTC | *Fix bug in fMRIVolume | 30 March 2013, 19:49:10 UTC |
| e760a93 | Matt Glasser | 30 March 2013, 18:55:46 UTC | *Apply MJ's warpfield edits to Diffusion Pipeline | 30 March 2013, 18:55:46 UTC |
| ce4b51d | Matt Glasser | 30 March 2013, 18:36:28 UTC | fMRISurface: *Remove all Caret5 dependencies and incorperate improved wb_command algorithms *Discuss how to handle unique parameters like spacings, turn off gradient distortion correction in example scripts *Convert external interfaces to "MJ Style" *Prepare example data, scripts, and documentation *CleanUp Variable Names for spin echo field map and FcMRI vs fMRI | 30 March 2013, 18:36:28 UTC |
| 15b8499 | Matt Glasser | 30 March 2013, 14:54:40 UTC | fMRIVolume: *Prepare example data, scripts, and documentation *Make it possible to skip gradient nonlinearity correction of fMRI data and spin echo field map *Delete FNIRT hacky correction *Use standard backwards differentiation for motion derivatives. *Some improvements to regular field map processing *Make use of motion correction mask for fMRI data in final masking step. *Don't write files to structural folders and use only two folders for processing | 30 March 2013, 14:54:40 UTC |
| 1d1e886 | Tony Wilson | 29 March 2013, 21:20:10 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 29 March 2013, 21:20:10 UTC |
| f569a43 | Matt Glasser | 29 March 2013, 21:00:14 UTC | *Fix PostFreeSurfer bug | 29 March 2013, 21:00:14 UTC |
| bedbd64 | Tony Wilson | 29 March 2013, 16:46:52 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 29 March 2013, 16:46:52 UTC |
| 7a7c66e | Matt Glasser | 29 March 2013, 16:20:03 UTC | *Fix previous commit to add greyordinates templates | 29 March 2013, 16:20:03 UTC |
| d55d7b6 | Tony Wilson | 29 March 2013, 16:09:30 UTC | default location to fsl5/bin/ changed to /data/standard/ | 29 March 2013, 16:09:30 UTC |
| e3c6918 | Matt Glasser | 28 March 2013, 04:46:19 UTC | PostFreeSurfer: *Convert external interfaces to "MJ Style" *Prepare example data, scripts, and documentation *Add aparc+aseg.mgz and aparc.a2009s+aseg.mgz to native and MNI volume spaces *Create brainordinates space in PostFreesurfer and make standard brainordinates space via copy *Make Stuctural Space 32k data *Make wmparc and ribbon label volumes that display correctly in workbench *Make 2mm T1w and T2w *Reduce smoothed myelin map smoothing to 4mm FWHM *Remove all Caret5 dependencies and incorperate improved wb_command algorithms -Improved resampling of data between surface meshes -Improved accuracy of downsampled surfaces -CIFTI dense scalar and label files available *Skyra bias corrected myelin maps *Convert surface atlases to .surf.gii format *Use CIFTI dense scalar and label files in the spec files | 28 March 2013, 04:46:19 UTC |
| 518ab3f | Matt Glasser | 21 March 2013, 22:02:52 UTC | FreeSurfer: *Depend on FreeSurfer 5.2 (remove specially compiled FreeSurfer binaries) *Convert external interfaces to "MJ Style" *Prepare example data, scripts, and documentation *Add openmp flag for recon-all to speed up mri_em_register and mri_ca_register *Remove all Caret5 dependencies and incorperate improved wb_command algorithms FreeSurfer: Converted to MJ Style Top Level Call ${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline.sh \ --subject="$Subject" \ --subjectDIR="$SubjectDIR" \ --t1="$T1wImage" \ --t1brain="$T1wImageBrain" \ --t2="$T2wImage" \ --printcom=$PRINTCOM | 21 March 2013, 22:02:52 UTC |
| 3aeb4b3 | Matt Glasser | 21 March 2013, 01:48:18 UTC | Pipeline Changes: PreFreeSurfer: *Replace initial structural image copy with fslreorient2std command so that users don't mess this up.. *Slightly improve FieldMap magnitude to structural registration by not using a brain mask *Reduce execution time and file sizes by using lower resolution warpfields *Prepare example data, scripts, and documentation *Remove all Caret5 dependencies and incorperate improved wb_command algorithms All: *Update wb_command Interface Changes: Global: Moved environment script to examples. You should use your own environment script based on it and not edit it in the gitRepo. Environment Variable Changed CARET7DIR=${HCPPIPEDIR}/global/binaries/caret7/bin_linux64 --> CARET7DIR=${HCPPIPEDIR}/global/binaries/caret7/bin_rh_linux64 PreFreeSurfer: *Remove $FieldMapImageFolder variable *Template path needs to be specified in the pipeline arguments for each template file, not in the pipeline environment *The same is true for the config file paths | 21 March 2013, 01:48:18 UTC |
| 49fefb2 | markj789 | 19 March 2013, 19:15:11 UTC | Added --rel and --relout flags to applywarp and convertwarp calls to force relative warp convention everywhere, with the one remaining exception being epi_reg that is explicitly converted afterwards, although in the future epi_reg will be changed in FSL | 19 March 2013, 20:48:05 UTC |
| c4783e2 | Tony Wilson | 14 March 2013, 22:19:16 UTC | setup changed | 19 March 2013, 20:44:00 UTC |
| 5160eac | Tony Wilson | 09 March 2013, 20:49:33 UTC | PreFS changes for NRG environment done. | 19 March 2013, 20:44:00 UTC |
| b71b77e | markj789 | 25 February 2013, 22:19:04 UTC | Added mask to mcflirt_acc | 19 March 2013, 20:43:48 UTC |
| b7140e8 | markj789 | 15 February 2013, 16:14:32 UTC | Created a SetUpHCPPipeline.sh file for environment variables and modified appropriate code in PreFS, fMRIVol and global to use these - suitable for WashU cluster or otherwise - and other pipelines should be modified later (current status of change is untested, but the change is quite simple) | 19 March 2013, 20:43:48 UTC |
| f5e3b58 | markj789 | 15 February 2013, 11:48:19 UTC | Major modification of many files based on Oxford code review; this version is what has successfully been tested on the Oxford system but is not yet modified to be suitable for the WashU cluster | 19 March 2013, 20:43:48 UTC |
| 1d8a89e | markj789 | 14 February 2013, 14:39:33 UTC | Just putting in one modified file to start with to see if this works | 19 March 2013, 20:36:19 UTC |
| 1d5e0d1 | Stam Sotiropoulos | 11 March 2013, 17:56:05 UTC | small correction on registering grad_dev to structural space | 11 March 2013, 17:56:05 UTC |
| 4d7360d | Stam Sotiropoulos | 06 March 2013, 15:06:58 UTC | Diffusion Pipeline Changes - Bring final data to structural ACPC space | 06 March 2013, 15:06:58 UTC |
| 6ce3d99 | Matt Glasser | 30 January 2013, 21:21:08 UTC | *Add brain masking (based on structural segmentation) to diffusion data at the end of the pipeline to reduce file size *Delete unused FLIRT FA to T1w registration, this was not as good as BBR b0 to T1w | 30 January 2013, 21:21:08 UTC |
| 606d6ad | Matt Glasser | 24 January 2013, 19:36:59 UTC | *Fix diffusion pipeline with new eddy version *Use supercomputer compiled topup to allow functional pipelines to run on the supercomputer | 24 January 2013, 19:36:59 UTC |
| e619ec8 | Stam Sotiropoulos | 24 January 2013, 17:21:40 UTC | changed fwhm for eddy's new binary | 24 January 2013, 17:21:40 UTC |
| d9f0828 | Tony Wilson | 24 January 2013, 03:35:09 UTC | fix for EMPTY | 24 January 2013, 03:35:09 UTC |
| ce700b7 | Tony Wilson | 15 January 2013, 18:01:49 UTC | updated diffusion usage | 15 January 2013, 18:01:49 UTC |
| e765bb3 | Matt Glasser | 11 January 2013, 16:40:29 UTC | *Actually fix previous commits | 11 January 2013, 16:40:29 UTC |
| befe20d | Matt Glasser | 11 January 2013, 16:19:29 UTC | *Change executable status of topup to executable | 11 January 2013, 16:19:29 UTC |
| ffea34d | Matt Glasser | 11 January 2013, 16:17:16 UTC | *Add back in previous version of topup | 11 January 2013, 16:17:16 UTC |
| f1bd9e8 | Matt Glasser | 11 January 2013, 16:16:08 UTC | *Delete topup | 11 January 2013, 16:16:08 UTC |
| 29099df | Matt Glasser | 10 January 2013, 21:54:20 UTC | *Revert Previous Commit *Use FSL 5.0.2 supercomputer compiled topup binary for compatability with supercomputer | 10 January 2013, 21:54:20 UTC |
