From 63078c8e5c6ef1a8cd183c9d09f1634f033a4a5a Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 30 Aug 2024 14:01:24 -0400 Subject: [PATCH] docs: reformat abbreviations --- docs/outputs.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/outputs.md b/docs/outputs.md index c60fa829..f27dfa47 100644 --- a/docs/outputs.md +++ b/docs/outputs.md @@ -1,6 +1,6 @@ # Outputs of *NiBabies* -*NiBabies* outputs conform to the :abbr:`BIDS (brain imaging data structure)` +*NiBabies* outputs conform to the {abbr}`BIDS (brain imaging data structure)` Derivatives specification (see `BIDS Derivatives`_, along with the upcoming `BEP 011`_ and `BEP 012`_). *NiBabies* generates three broad classes of outcomes: @@ -460,7 +460,7 @@ of possible confounds, which enable researchers to choose the most suitable deno strategy for their downstream analyses. Confounding variables calculated in *NiBabies* are stored separately for each subject, -session and run in :abbr:`TSV (tab-separated value)` files - one column for each confound variable. +session and run in {abbr}`TSV (tab-separated value)` files - one column for each confound variable. Such tabular files may include over 100 columns of potential confound regressors. :::{danger} @@ -677,7 +677,7 @@ The procedure essentially follows the initial proposal of the approach by Patria The visual reports provide several sections per task and run to aid designing a denoising strategy for subsequent analysis. Some of the estimated confounds are plotted with a "carpet" visualization of the -:abbr:`BOLD (blood-oxygen level-dependent)` time series [^Power2016]. +{abbr}`BOLD (blood-oxygen level-dependent)` time series [^Power2016]. Noise components computed during each CompCor decomposition are evaluated according to the fraction of variance that they explain across the nuisance ROI. @@ -693,7 +693,7 @@ Also included is a plot of correlations among confound regressors. This can be used to guide selection of a confound model or to assess the extent to which tissue-specific regressors correlate with global signal. -See implementation on :mod:`~nibabies.workflows.bold.confounds.init_bold_confs_wf`. +See implementation on . ## References