Chris Markiewicz

Symbolic links are resolved unnecessarily

4

### Describe the bug Sphinx has a number of places where it uses `Path.resolve()` to normalize paths. I assume this is because `pathlib.Path()` doesn't have any method of normalizing `..`...

fix: Calculate premask from BOLD when sbref is provided

1

Paired with nipreps/niworkflows#1001, attempt to fix nipreps/niworkflows#1000.

For single-echo (ds054) we currently have: * [sub-100185_task-machinegame_run-01_desc-preproc_bold.json](https://output.circle-artifacts.com/output/job/0309e33f-75f6-49a3-a342-f68ea3c42fd4/artifacts/0/tmp/ds054/fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json) ```json { "RepetitionTime": 1.0, "SkullStripped": false, "SliceTimingCorrected": false, "Sources": [ "bids:raw:sub-100185/func/sub-100185_task-machinegame_run-01_bold.nii.gz" ], "TaskName": "Machine Game" } ``` It should be: ```diff {...

This metadata file currently has: ```json { "Sources": [ "bids:raw:sub-100185/func/sub-100185_task-machinegame_run-01_bold.nii.gz", "bids::sub-100185/func/sub-100185_task-machinegame_run-01_desc-coreg_boldref.nii.gz", "bids::sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt", "bids::sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt", "bids::sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt" ] } ``` It should be: ```diff { "Sources": [ - "bids:raw:sub-100185/func/sub-100185_task-machinegame_run-01_bold.nii.gz", "bids::sub-100185/func/sub-100185_task-machinegame_run-01_desc-coreg_boldref.nii.gz", - "bids::sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt", -...

This metadata file currently has: ```json { "Sources": [ "bids:raw:sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_bold.nii.gz", "bids:raw:sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_bold.nii.gz", "bids:raw:sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_bold.nii.gz", "bids::sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz", "bids::sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt", "bids::sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt", "bids::sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt", "bids:anat:sub-02/anat/sub-02_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5", "bids:templateflow:tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz" ] } ``` It should be: ```json { "Sources": [ - "bids:raw:sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_bold.nii.gz",...

BIDS Derivatives files SHOULD have a list of URIs to their sources. These should always be findable files, either in an input dataset (including templateflow) or in the current output...

## Summary This PR aims to ensure that we handle files/directories with spaces correctly. Unfortunately, there are a number of interfaces that separately handle the problem by including quotes in...

BEP 038 (Atlases and Templates) is currently under community review: * https://github.com/bids-standard/bids-specification/discussions/2250 Please review the changes carefully, participate in the discussion, and vote before November 21! Note that votes cannot...

[ENH] Allow datacite.yml in dataset root

1

The DataCite Metadata Schema (https://schema.datacite.org/meta/kernel-4/) is a fairly comprehensive structure for describing citable datasets, including [contributors](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/contributor/) (including [organizations](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/contributor/#a-nametype) and contributor [roles](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/contributor/#a-contributortype)), [funders](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/fundingreference/), [licenses](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/rights/) and [abstracts](https://datacite-metadata-schema.readthedocs.io/en/4.6/properties/description/). The DataCite Metadata Working Group...

Companion to #2221, adding JSON-Schema files for use in the BIDS validator.