pybids

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How to treat `n/a` in events

1

Consider a variable like response time, that only has meaning if a response is made. If it's not made, there is nothing to model. onset | duration | trial_type |...

effigies

What are the possible kinds of associations?

1

I'd like to filter the output of `get_associations()` by kind. Unfortunately, I fail to find any documentation on the association kinds. There is some info in #431 but it's not...

mateuszpawlik

Analysis.setup() cannot handle if `Run` is not defined in StatsModel

1

In a scenario where subjects have 1-2 runs (with those w/ only 1 run having no run labels), `Analysis.setup()` crashes when the statsmodel doesn't define `Run` under `Input`: ``` ERROR:nipype.workflow:could...

adelavega

ENH: Add warning when loading old db

1

To address loading incompatible saved dbs from previous various we could: - Throw a warning when loading a db from a previous pybids version - Catch SQL exceptions and suggest...

adelavega

SQLAlchemy 1.4 migration

1

Apparently SQLAlchemy is undergoing a massive refactor for version 2.0, and is using 1.4 as a stepping stone. The idea seems to be break some things, let people fix them...

effigies

BIDS Analysis: Make selectors more specific

5

Currently, if I want to have an analysis run for subject 1, run 1 and subject 2 run 2, it's not possible as the following specified subject 1+2 runs 1+2,...

adelavega

Currently, the `config` argument passed at `BIDSLayout` initialization isn't passed through to `add_derivatives()` when there are derivatives present; instead, `None` is passed. The ostensible reason for this is so that...

tyarkoni

Indexing associations between files (e.g., identifying `*_events.tsv` that inform a `*.nii.gz` BOLD run) is quite expensive and not useful to most people. We should add an initialization flag that disables...

tyarkoni

Support incremental indexing

3

Suppose I have a BIDSLayout. I then do some processing and generate new files, which I'd like to add back into the layout so later steps know they are there....

hbraunDSP

'RunNode' object has no attribute 'get_collections'

5

``` In [1]: from bids.layout import BIDSLayout In [2]: layout = BIDSLayout('/datasets/raw/SherlockMerlin/', derivatives=True) In [3]: layout.get_collections(subject='19', task='MerlinMovie', level='run') ``` Throws the following error: ``` /usr/local/lib/python3.6/site-packages/bids/layout/layout.py in get_collections(self, level, types, variables,...

adelavega