mwaskom / lyman

Data pipelines and analysis library for functional MRI

http://www.cns.nyu.edu/~mwaskom/software/lyman

mwaskom/lyman Issues

Add API documentation
Closed 4 years ago
Add FIR model in glm
Closed 4 years ago1
Move GammaHRF to GammaBasisHRF, add single-variate version
Closed 4 years ago1
Seperate out distortion estimation and cache results
Updated 4 years ago
Add option to write time series qc movies as mp4
Updated 5 years ago1
Add docs for previous releases
Closed 6 years ago5
Nuisance regressors could get a second round of dimensionality reduction
Updated 5 years ago2
FD line plot in carpet plot does not adapt upper y limit to large movements
Closed 5 years ago1
Nodes that use convert binary consume > 100% CPU
Closed 5 years ago
Condition names that parse to numerics break in model specification
Closed 5 years ago
Switch to using MPLBACKEND for testing
Closed 5 years ago1
Future warnings about numpy indexing changes
Closed 5 years ago1
Rename anatomical "template" workflow/outputs to "segment"
Updated 5 years ago
session-wise preproc gets repeated when each session has multiple experiments
Updated 5 years ago2
Make it easier to have a single default model
Updated 5 years ago
Add confound identification/removal
Updated 5 years ago1
Incorporate FIR model in to workflows
Closed 5 years ago1
Change order of processing in fit model to fail earlier with bad design
Closed 5 years ago1
Revisit grand mean target
Closed 5 years ago
image_to_matrix docstring is incorrect
Closed 5 years ago
Add titles to some QC plots
Closed 5 years ago
(Optionally) save session-wise results
Updated 5 years ago
data_dictionary definition unclear that lyman requires the output of freesurfer recon-all
Closed 6 years ago1
Add set_subjects_dir method
Updated 6 years ago
Model design file names are not expected to have the experiment name prepended
Closed 6 years ago
API inconsistencies
Updated 6 years ago
Better error from workflows when LYMAN_DIR is not defined
Updated 6 years ago
Add results interface objects
Updated 6 years ago
Support for input datasets formatted according to BIDS
Closed 6 years ago2
seg and surf files do not agree about what is cortex
Closed 7 years ago
Anatomical processing planning
Updated 7 years ago
Model workflow crashes when hpf_cutoff is None
Closed 7 years ago
Model workflow crashes when contrast is not defined in contrast file
Closed 7 years ago
Handle single-session experiments without specifying session
Closed 7 years ago1
Loading experiment info raises when model-level params are defined
Closed 7 years ago
YAML load parses dates into datetime objects, not strings
Closed 7 years ago
Add gif looping over each run's mean mosaic to session-level qc
Updated 7 years ago
Handle contrasts properly across model workflows
Closed 7 years ago
Add regional gls model
Updated 7 years ago
Save parameters to output directories
Closed 7 years ago
Implement new info specs
Closed 7 years ago
Complete overhaul of lyman command line interface
Closed 7 years ago
Batch renaming
Closed 7 years ago
Implement new modelling workflow
Closed 7 years ago
Add Jacobian correction after distortion unwarping
Closed 7 years ago
Define template space based on anatomy only
Closed 7 years ago
Implement cross-experiment templates
Closed 7 years ago7
Reconsider output hierarchy order
Closed 7 years ago1
Add preprocessing for experiments without spin-echo fieldmaps
Updated 7 years ago
Consider adding B1- bias field removal in preprocessing
Updated 7 years ago