pybids

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See https://github.com/nipreps/fmriprep/issues/2313. Here, when we create or reset a database, we should catch SQL errors and note the location of the file.

effigies

add very basic visualization of events file to pybids

5

(Discussed by email with @oesteban and @tyarkoni before deciding to open the issue in this repo) TL;DR a suggestion to add enhance pybids to do basic visulation of events file...

Remi-Gau

pybids error running cifti output from fmriprep in fitlins

7

I've been trying to run cifti files from fmriprep 20.2.0rc0 through fitlins 0.7.0 but have been hitting some errors, the most recent from pybids: `KeyError: "Metadata term 'RepetitionTime' unavailable for...

jsmentch

get_metadata() outputs empty dictionary

1

I followed the [tutorial for pybids](https://bids-standard.github.io/pybids/layout/index.html) and just copy-pasted the code from the tutorial into a script: ``` from os.path import join from bids import BIDSLayout from bids.tests import get_test_data_path...

JohannesWiesner

adding write capabilities to pybids

2

Since I have been working on a couple of matlab functions to write some basics BIDS things while running experiments I figured I would open an issue here to see...

Remi-Gau

This may be premature, but in https://github.com/bids-standard/bids-specification/pull/475 we are attempting to build a machine-readable version of the specification that can be versioned and pulled in for other packages, like `pybids`...

tsalo

derivatives=True breaks BIDSLayout

5

``` from pathlib import Path from bids import BIDSLayout import bids for i in range(10): layout = BIDSLayout(Path(bids.__file__).parent / "tests" / "data" / "7t_trt", database_path=(Path.home()), derivatives=True, reset_database=True) print(layout.entities["subject"].count()) ``` gives...

christian-oreilly

Request documentation for layout Config

3

BIDSLayout has 2 relevant kwargs: ``` config : str or list or None, optional Optional name(s) of configuration file(s) to use. By default (None), uses 'bids'. config_filename : str Optional...

cboulay

Missing data in get_collections(level='session')

5

I think this is a bug, anyway: Reproduction: ``` $ datalad clone ///openneuro/ds000224 $ datalad get -C ds000224 sub-MSC01/func01 $ cat ds000224/sub-MSC01/ses-func01/sub-MSC01_ses-func01_scans.tsv filename acq_time func/sub-MSC01_ses-func01_task-rest_bold.nii.gz 1894-08-25T01:15:37 func/sub-MSC01_ses-func01_task-memorywords_bold.nii.gz 1894-08-25T02:20:34 func/sub-MSC01_ses-func01_task-memoryfaces_bold.nii.gz 1894-08-25T02:31:57...

effigies

Entities above dataset root are extracted

3

If I have a dataset whose name is (for reasons I can get into): `.../sub-03/sourcedata/`, then all files inside that dataset will be responsive to a request for `sub-03`, even...

effigies