| 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 |
| 24620a9 | Matt Glasser | 10 January 2013, 21:46:19 UTC | *Depend on FSL 5.0.2 *Use topup provided by FSL | 10 January 2013, 21:46:19 UTC |
| d9f85d2 | Matt Glasser | 06 January 2013, 19:17:02 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 06 January 2013, 19:17:02 UTC |
| 23e07fc | Matt Glasser | 06 January 2013, 19:15:33 UTC | *Reverse white and pial surface order in file conversion loop to make the white topology be the one used in subsequent files in case the pial topology is reversed | 06 January 2013, 19:15:33 UTC |
| dc9ee76 | Tony Wilson | 25 December 2012, 17:51:40 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 25 December 2012, 17:51:40 UTC |
| 9b7ef40 | Tony Wilson | 24 December 2012, 21:30:27 UTC | changed diffpreproc to handle /path/to/nifti/EMPTY | 24 December 2012, 21:30:27 UTC |
| 681cd4c | Stam Sotiropoulos | 13 December 2012, 16:28:30 UTC | Minor changes | 13 December 2012, 16:28:30 UTC |
| aee93b3 | Stam Sotiropoulos | 10 December 2012, 22:11:00 UTC | Remove negative intensity values from final diffusion data | 10 December 2012, 22:11:00 UTC |
| 41a7c2d | Tony Wilson | 28 November 2012, 20:07:52 UTC | removed , replaced with suitable variables | 28 November 2012, 20:07:52 UTC |
| 92677dc | Matt Glasser | 24 November 2012, 07:09:27 UTC | *Changed FreeSurfer Pipeline Queue in Examples | 24 November 2012, 07:09:27 UTC |
| e47765b | Matt Glasser | 22 November 2012, 13:36:53 UTC | *Make example scripts use ${GitRepo} caret_command and wb_command | 22 November 2012, 13:36:53 UTC |
| 842df82 | Matt Glasser | 20 November 2012, 21:31:34 UTC | *Comply with supercomputer python requirements | 20 November 2012, 21:31:34 UTC |
| 11062e9 | NRGadmin | 15 November 2012, 20:24:59 UTC | Eddy updated to newest version from Oxford. Built on NRG cluster (CentOS 6) | 15 November 2012, 20:24:59 UTC |
| 8735610 | Tony Wilson | 13 November 2012, 18:39:23 UTC | fsl5 version of eddy updated | 13 November 2012, 18:39:23 UTC |
| 3ddcc47 | Stam Sotiropoulos | 13 November 2012, 11:33:47 UTC | Changes in diffusion pipeline to include corrections in gradient_unwarp.py | 13 November 2012, 11:33:47 UTC |
| 673ca6a | Stam Sotiropoulos | 11 November 2012, 18:18:15 UTC | Call eddy,topup and applytopup from $globaldir | 11 November 2012, 18:38:04 UTC |
| 9e52d6b | Matt Glasser | 09 November 2012, 21:35:53 UTC | *Update wb_command to make sure that it gives an error status and reports the error to StdErr if it fails *Add some jitter (1s) to Example pipeline scripts to prevent two jobs from trying to write to the same file at the same time (i.e. make sure that the internal pipeline checks for this actually work) | 09 November 2012, 21:35:53 UTC |
| 600b413 | Matt Glasser | 08 November 2012, 19:52:56 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 08 November 2012, 19:52:56 UTC |
| 032f91f | Matt Glasser | 08 November 2012, 19:33:50 UTC | *Update wb_command to current version compiled on Wash U Supercomputer | 08 November 2012, 19:33:50 UTC |
| 6048fc1 | Tony Wilson | 08 November 2012, 18:42:58 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 08 November 2012, 18:42:58 UTC |
| ebbe2b8 | Tony Wilson | 08 November 2012, 18:42:12 UTC | changed permissions from 644 to 755 | 08 November 2012, 18:42:12 UTC |
| a6b95e4 | Matt Glasser | 08 November 2012, 18:16:38 UTC | *Bump gradient unwarping version to 2.0.0alpha-hcp-1 | 08 November 2012, 18:16:38 UTC |
| 82dce9f | Matt Glasser | 08 November 2012, 17:09:11 UTC | *Fix gradient unwarping code for oblique volumes | 08 November 2012, 17:09:11 UTC |
| f5479a1 | Matt Glasser | 08 November 2012, 08:03:24 UTC | *Cleanup of deleted files | 08 November 2012, 08:03:24 UTC |
| aaf7b84 | Matt Glasser | 08 November 2012, 08:00:10 UTC | *Finish previous commit | 08 November 2012, 08:00:10 UTC |
| 773ad50 | Matt Glasser | 08 November 2012, 07:57:53 UTC | *Remove unnecessary external dependancies. Dependencies limited to FSL 5.0.1, FreeSurfer 5.1, and gradient unwarping code *Add FSL 5.0.1+ binaries to GitRepo/global/binaries (topup, applytopup, eddy) *Fix white space difference between Motion_Regressors.txt and Motion_Regressors_dt.txt *rename trendout.awk to mtrendout.awk for consistency with 4dfp tools *Set palette for MNINonLinear registration Jacobian volume *Final bugfixes for example data and scripts *Add Readme.txt *Add gradient unwarping source code to git repository (will be updated with Marks changes when ready) *Remove references to non-installed gradient unwarping code (these did not do anything anyway) *Fix color bar display of myelin maps and thickness maps (display only positive) | 08 November 2012, 07:57:53 UTC |
| 7070398 | Matt Glasser | 07 November 2012, 18:56:01 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 07 November 2012, 18:56:01 UTC |
| bcfb989 | Matt Glasser | 07 November 2012, 18:54:57 UTC | *Fix more typos in example script | 07 November 2012, 18:54:57 UTC |
| beb0930 | Matt Glasser | 07 November 2012, 16:33:32 UTC | *Fix typo in examples scripts | 07 November 2012, 16:33:32 UTC |
| aba5d63 | Stam Sotiropoulos | 07 November 2012, 14:06:04 UTC | Changes for handling incomplete scans | 07 November 2012, 14:09:09 UTC |
| 99a252a | Matt Glasser | 06 November 2012, 18:18:44 UTC | *Initial Commit of Revised Examples including Examples/Scripts, which has example batch scripts that could be run on the example subject, Examples/792564. Some bugs are possible in this initial commit. | 06 November 2012, 18:18:44 UTC |
| 556b1bf | Matt Glasser | 06 November 2012, 06:58:23 UTC | *Fix intensity normalization of fMRIVolume to be global 4D rather than framewise 3D *Fix comment of currently unused code | 06 November 2012, 06:58:23 UTC |
| 2d4929e | Stam Sotiropoulos | 05 November 2012, 10:02:48 UTC | Changed permissions | 05 November 2012, 10:02:48 UTC |
| 2f33bc2 | Stam Sotiropoulos | 02 November 2012, 11:28:13 UTC | Prepare flags for next version of eddy | 02 November 2012, 11:28:13 UTC |
| 43f3f65 | Stam Sotiropoulos | 02 November 2012, 11:25:54 UTC | Slight changes to applytopup | 02 November 2012, 11:25:58 UTC |
| 69b92ff | Matt Glasser | 31 October 2012, 20:10:14 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 31 October 2012, 20:10:14 UTC |
| 10ca773 | Matt Glasser | 31 October 2012, 20:07:55 UTC | *Change matlab code comment in motion derivative calculation (no actual change to code, just to comment) | 31 October 2012, 20:07:55 UTC |
| 10ef620 | Stam Sotiropoulos | 31 October 2012, 14:33:20 UTC | Correct typos | 31 October 2012, 14:33:20 UTC |
| c469537 | Stam Sotiropoulos | 31 October 2012, 11:45:57 UTC | Correct a bug during series rescaling in basic_preproc. Also slight changes to the DiffPipeline interface | 31 October 2012, 11:45:57 UTC |
| ae7ec00 | Matt Glasser | 29 October 2012, 23:11:00 UTC | *Remove Jacobian modulation and instead output the Jacobian in 2mm MNI space ${fMRIName}_Jacobian.nii.gz so that users can decide to apply it or not as desired. | 29 October 2012, 23:11:00 UTC |
| 539102e | Matt Glasser | 26 October 2012, 23:31:07 UTC | *Update topup/applytopup to latest versions that produce more accurate fields *Rewrite EPI distortion correction to occur separately from EPI to T1w registration at Jesper's suggestion (SBRef registered with FLIRT 6 dof to appropriate Spin echo image, then FSL generic warp field from topup applied). EPI to T1w registration now happens afterwards on the undistorted image (FLIRT BBR+bbregister) *Use Jacobian modulation (Jacobian field calculated by topup) to reduce intensity differences between the phase encoding directions due to compression and rarifaction of the data (note that Jacobian modulation is not implemented for regular field maps) to produce images with more symmetrical intensities | 26 October 2012, 23:31:07 UTC |
| 6cab6e7 | Matt Glasser | 10 October 2012, 02:59:54 UTC | Merge branch 'master' of github.com:Washington-University/Pipelines | 10 October 2012, 02:59:54 UTC |
| bb4c40a | Matt Glasser | 10 October 2012, 02:54:12 UTC | *Fix Caret5 caret_command to properly report exit status error and errors to stderr on -file-convert failures to make pipelines fail on error properly | 10 October 2012, 02:54:12 UTC |
| 553241e | Stam Sotiropoulos | 24 September 2012, 19:04:06 UTC | Small correction to basic_preproc | 24 September 2012, 19:04:06 UTC |
| ba32517 | Stam Sotiropoulos | 24 September 2012, 18:22:46 UTC | Added module that rescales series to match baseline intensities | 24 September 2012, 18:22:46 UTC |
| 5549d50 | Matt Glasser | 10 September 2012, 14:53:34 UTC | *Avi bugfix for trendout.awk | 10 September 2012, 14:53:34 UTC |
| 9feea23 | Matt Glasser | 10 September 2012, 03:58:47 UTC | *Update trendout.awk to remove mean (Steve S., Avi) | 10 September 2012, 03:58:47 UTC |
