Ecosyste.ms: Issues

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GitHub / mwaskom/lyman issues and pull requests

#100 - Fix travis build

Pull Request - State: closed - Opened by mwaskom over 7 years ago

#99 - Add Freeview wrapper script for checking registration quality

Pull Request - State: closed - Opened by mwaskom over 7 years ago - 1 comment

#98 - Change how cache directory is removed

Issue - State: closed - Opened by mwaskom over 7 years ago

#97 - Add polynomial regressors to design matrix

Issue - State: open - Opened by mwaskom over 7 years ago
Labels: Overhaul-2017

#96 - Slice time correction is being skipped

Issue - State: closed - Opened by mwaskom over 7 years ago - 1 comment

#95 - Images should be re-masked after registration

Issue - State: closed - Opened by mwaskom over 7 years ago - 1 comment

#93 - calculate_sat_point could be updated to account for surface stats

Issue - State: closed - Opened by sgagnon over 7 years ago - 6 comments

#92 - Additional denoising

Issue - State: closed - Opened by mwaskom almost 8 years ago - 1 comment

#91 - Plans for changes to lyman registration

Issue - State: closed - Opened by mwaskom almost 8 years ago - 9 comments

#90 - multiple sessions and field maps

Issue - State: closed - Opened by iancballard almost 8 years ago - 2 comments

#89 - Broken documentation url in README file

Issue - State: closed - Opened by himito almost 8 years ago

#88 - Remove lyman.mvpa module

Pull Request - State: closed - Opened by mwaskom over 8 years ago

#87 - lyman .08 issue

Issue - State: closed - Opened by iancballard over 8 years ago - 5 comments

#86 - Update parallel for Jupyter notebooks in maskfactory

Pull Request - State: closed - Opened by sgagnon over 8 years ago - 1 comment

#85 - "whole_brain" error

Issue - State: closed - Opened by sansplot over 8 years ago - 1 comment

#84 - Line 48 in surface_snapshots.py

Issue - State: closed - Opened by sgagnon over 8 years ago - 1 comment

#83 - Changes in IPython parallel cause an error when there is an error in make_masks

Issue - State: closed - Opened by mwaskom almost 9 years ago - 1 comment

#82 - Save func2anat registration matrix to reg directory for epi registrations

Pull Request - State: closed - Opened by mwaskom almost 9 years ago

#81 - bbregister workflow thought

Issue - State: closed - Opened by iancballard almost 9 years ago - 1 comment

#80 - ANTs naming conventions

Issue - State: closed - Opened by iancballard about 9 years ago - 2 comments

#79 - Error with -altmodel

Issue - State: closed - Opened by rainbowcnh about 9 years ago - 1 comment

#78 - Registration workflow crashes when registering model outputs with no design

Issue - State: closed - Opened by mwaskom about 9 years ago - 1 comment

#77 - Write grand mean image out from fixed effects workflow

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#76 - Increased flexibility for confound removal during model fitting.

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#75 - Improve memory efficiency in model summary functions

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#74 - Add ability to correct susceptibility-induced distortions

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#72 - subject specific experiment files?

Issue - State: closed - Opened by mwaskom about 9 years ago - 1 comment

#71 - Improve surface snapshots

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#70 - Allow for conditions with no events

Pull Request - State: closed - Opened by mwaskom about 9 years ago

#69 - Add cross-experiment epi space registration

Pull Request - State: closed - Opened by mwaskom over 9 years ago

#68 - confounds

Issue - State: closed - Opened by iancballard over 9 years ago - 1 comment

#67 - Improve the anatomy snapshots script

Pull Request - State: closed - Opened by mwaskom over 9 years ago

#66 - Update model workflow for compatability with newer FSL

Pull Request - State: closed - Opened by mwaskom over 9 years ago - 2 comments

#65 - clarification question about design files

Issue - State: closed - Opened by iancballard over 9 years ago - 6 comments

#64 - bug and fix?

Issue - State: closed - Opened by iancballard over 9 years ago - 1 comment

#63 - WIP Add FIR Model Setup Options

Pull Request - State: closed - Opened by kastman over 9 years ago - 4 comments

#62 - missing runs

Issue - State: closed - Opened by iancballard over 9 years ago - 5 comments

#61 - motion regressors

Issue - State: closed - Opened by iancballard over 9 years ago - 5 comments

#60 - issue with run_warp and ANTS

Issue - State: closed - Opened by iancballard over 9 years ago - 5 comments

#59 - confusing error

Issue - State: closed - Opened by iancballard over 9 years ago - 2 comments

#58 - bug with just 1 subject

Issue - State: closed - Opened by iancballard over 9 years ago - 2 comments

#57 - Add support for subjects that are missing instances of some conditions

Issue - State: closed - Opened by boydmeredith over 9 years ago - 9 comments

#56 - anatomy_snapshots.py using increasingly more RAM

Issue - State: closed - Opened by januz over 9 years ago - 2 comments

#55 - Add crash_dir variable to project level parameterization.

Pull Request - State: closed - Opened by mwaskom over 9 years ago

#54 - Fix comment spelling error in run_fmri.py

Pull Request - State: closed - Opened by sgagnon over 9 years ago - 3 comments

#53 - Add residual timeseries registration.

Pull Request - State: closed - Opened by mwaskom almost 10 years ago

#52 - Fix for FSL highpass filter changes

Pull Request - State: closed - Opened by mwaskom almost 10 years ago

#51 - SampleToSurface crash with run_group.py

Issue - State: closed - Opened by dgdillon almost 10 years ago - 3 comments

#50 - Newest version of FSL leads to different SNR values

Issue - State: closed - Opened by valeriecarr almost 10 years ago - 1 comment

#49 - Gives "missing dependencies: seaborn" although it is installed

Issue - State: closed - Opened by januz almost 10 years ago - 2 comments

#48 - Fix bug in FNIRT workflow datasink

Pull Request - State: closed - Opened by mwaskom almost 10 years ago

#47 - filename change in output of run_warp.py needed?

Issue - State: closed - Opened by Crisly almost 10 years ago - 5 comments

#45 - Add basic travis build

Pull Request - State: closed - Opened by mwaskom about 10 years ago

#44 - add pause to surface_snapshots

Pull Request - State: closed - Opened by sgagnon about 10 years ago - 2 comments

#43 - Use smarter masks derived from the anatomy

Issue - State: closed - Opened by mwaskom about 10 years ago - 1 comment

#42 - Model generation

Issue - State: closed - Opened by Crisly about 10 years ago - 9 comments

#41 - Add coreg_init to experiment file

Pull Request - State: closed - Opened by mwaskom about 10 years ago

#40 - The main model R squared should include temporal derivatives

Issue - State: closed - Opened by mwaskom over 10 years ago - 1 comment

#39 - Fixed effects level SNR looks to be calculated wrong

Issue - State: closed - Opened by mwaskom over 10 years ago - 2 comments

#38 - Style power spectrum report with whitegrid

Issue - State: closed - Opened by mwaskom over 10 years ago

#37 - Add unified ROI extraction

Issue - State: closed - Opened by mwaskom over 10 years ago - 1 comment

#35 - Add saving and registration of residual timeseries

Issue - State: closed - Opened by mwaskom over 10 years ago - 1 comment

#34 - Better fixed effects

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#33 - Better model

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#32 - Improvements and tweaks to the preprocessing workflow

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#31 - Better mixed effect model report

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#30 - Use ANTS for volume normalization

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#29 - Import from nipype.interfaces in workflows

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#28 - FLAMEO style differences between fixedfx and mixedfx

Issue - State: closed - Opened by TDaltonC over 10 years ago - 2 comments

#27 - Add option to take top <n> voxels in make_masks.py

Pull Request - State: closed - Opened by mwaskom over 10 years ago

#26 - Add option to erode volume ROIs in mask factory.

Pull Request - State: closed - Opened by toddt over 10 years ago

#25 - Add option to erode volume ROIs in MaskFactory, and generate WM, Ventric...

Pull Request - State: closed - Opened by toddt over 10 years ago

#24 - Feature request -- run model without conditions

Issue - State: closed - Opened by toddt over 10 years ago - 1 comment

#22 - Support arbitrary regressors of interest in timeseries model

Pull Request - State: closed - Opened by mwaskom almost 11 years ago

#21 - Add conjunction b/w anatomy and zstat in make_masks.py

Issue - State: closed - Opened by mwaskom almost 11 years ago - 1 comment

#20 - Add surface-based processing and visualization at the group level

Pull Request - State: closed - Opened by mwaskom almost 11 years ago

#19 - Runs are 0-based in evoked, but 1-based elsewhere

Issue - State: closed - Opened by mwaskom almost 11 years ago

#18 - R squared colormaps could be improved

Issue - State: closed - Opened by mwaskom almost 11 years ago

#17 - Rotate confound correlation x axis labels

Issue - State: closed - Opened by mwaskom almost 11 years ago

#16 - Preproc directories for altmodels should be relative links

Issue - State: closed - Opened by sgagnon about 11 years ago

#15 - fixed subject loop for altmodel

Pull Request - State: closed - Opened by sgagnon about 11 years ago - 1 comment

#14 - Hotfix for zero-variance voxels will break coef extraction

Issue - State: closed - Opened by mwaskom about 11 years ago

#13 - Timeseries reg only sinks functional mask for run 1

Issue - State: closed - Opened by mwaskom about 11 years ago - 1 comment

#12 - Major rewrite of the Nipype workflows (with smaller associated changes)

Pull Request - State: closed - Opened by mwaskom about 11 years ago

#10 - run_group.py does not use the default experiment

Issue - State: closed - Opened by mwaskom over 11 years ago

#9 - edited path directories for dof files

Pull Request - State: closed - Opened by sgagnon over 11 years ago

#8 - edited file structure for dof files

Pull Request - State: closed - Opened by sgagnon over 11 years ago

#7 - fixing cluster_to_rst imports

Pull Request - State: closed - Opened by sgagnon over 11 years ago

#6 - Freesurfer data is getting converted to nifti multiple times

Issue - State: closed - Opened by mwaskom over 12 years ago - 1 comment

#5 - experiments/template.py is out of date

Issue - State: closed - Opened by mwaskom over 12 years ago

#4 - Allow for default experiment in project.py

Issue - State: closed - Opened by mwaskom over 12 years ago

#3 - design correlation labels are wrong when derivatives are used

Issue - State: closed - Opened by mwaskom over 12 years ago - 1 comment

#2 - run_warp.py does not remove working_dir

Issue - State: closed - Opened by mwaskom over 12 years ago

#1 - Datasink run directories are not zero-padded

Issue - State: closed - Opened by mwaskom over 12 years ago - 1 comment