pybids

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in my recent PR, i ran into the issue that there was many spots where an invalid model would lead to an ugly crash. i started adding logic to catch...

adelavega

[pybids-core] Loading BIDSLayout with a path to a derivative folder

1

In one of the unit tests, a `BIDSLayout` is created using a derivative path: ``` def test_dataset_missing_generatedby_fails_validation(self): dataset_path = Path("ds005_derivs", "format_errs", "no_pipeline_description") with pytest.raises(BIDSDerivativesValidationError): BIDSLayout(Path(get_test_data_path())/dataset_path) ``` The expectation is to...

erdalkaraca

Jeannette reported that run and scan numbers were not available to the model & transformations.

adelavega

cannot access the 'group' variable in 'participants.tsv' in the narps dataset https://github.com/jdkent/model-zoo/tree/typical/narps [this line](https://github.com/jdkent/model-zoo/blob/9f43fb064bec800a3680df86e50a085d30e4ee1c/narps/NARPS_model.py#L116) this output: ``` --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Input In [60], in () 1...

jdkent

Intercept only first level models throw an error

1

Running an intercept only first level model throws an error: `TypeError: reduce() of empty sequence with no initial value` To reproduce: ``` import pandas as pd import numpy as np...

Shotgunosine

This PR is a work in progress and should remain open for the time being. ### Objective The `BIDSLayout` has long been known to have performance issues on large datasets...

gkiar

adelavega

Evaluate ancpbids as a successor to bids.layout

18

The [ancpbids](https://github.com/ANCPLabOldenburg/ancp-bids) project has made formidable progress in implementing a `BIDSLayout`-like API, with marked performance improvements, using a different underlying implementation with a custom query language. Given limited resources to...

adelavega

suggesting to add a transformation that provides the temporal derivative of given input column. The following is copied and pasted from a draft of the PyBIDS transformations specification, but this...

sjshim

StatsModels: Make `group_by` mandatory

1

Given that for simple models (i.e. contrasts at run level, and dummy contrasts at subject and dataset level) `GroupBy` must be set, I can't imagine a situation where letting pybids...

adelavega