From 625fffd83e4b9dffd73de83b5a2d1976110ec370 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Fri, 6 Oct 2023 11:31:51 +0200 Subject: [PATCH] add links --- src/outputs.md | 2 +- src/scope.md | 2 +- src/specification.md | 12 ++++++------ 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/outputs.md b/src/outputs.md index 3155e90..a529402 100644 --- a/src/outputs.md +++ b/src/outputs.md @@ -86,7 +86,7 @@ datasets. When generated, an execution report that completely describes the processing that was executed and the dataset MUST comply with the BIDS Provenance Extension Proposal (BEP28). These outputs are OPTIONAL, and if provided, should be -specified in the `output-files` section of the tool descriptor. +specified in the [`output-files`](./outputs.md) of the tool descriptor. Similarly, the dataset_description.json file SHOULD be updated to reflect the processing that has occurred by the BIDS Application. diff --git a/src/scope.md b/src/scope.md index bfd29ad..26bf523 100644 --- a/src/scope.md +++ b/src/scope.md @@ -38,7 +38,7 @@ which were described in Gorgolewski, et al. 2017 (doi:[10.1371/journal.pcbi.1005209](https://doi.org/10.1371/journal.pcbi.1005209)), here referred to as BIDS-Apps 1.0. Backwards compatibility with BIDS-Apps 1.0 is not an explicit goal, but can be achieved in many cases as is discussed in -Section [3.1.2.1](#3-1-2-1-backwards-compatibility-9). A summary of changes from +the section [on backwards-compatibility](./inputs#backwards-compatibility). A summary of changes from BIDS-Apps 1.0 is included in the [CHANGELOG](./CHANGELOG.md#0.1.0.dev). This specification is seen as complementary to BIDS-Derivatives, which is part diff --git a/src/specification.md b/src/specification.md index b07a27a..eca215b 100644 --- a/src/specification.md +++ b/src/specification.md @@ -6,15 +6,15 @@ There are three domains of requirements that BIDS Applications must specify: 1. Required application behaviors 1. Required application outputs -BIDS contains "required", "recommended" and "optional" fields. These are -indicated throughout the document: +BIDS contains "required", "recommended" and "optional" fields. +These are indicated throughout the document: - **REQUIRED**: essential to be BIDS compliant (meaning MUST as per RFC2199) - **RECOMMENDED**: gives a warning if not present (meaning SHOULD as per RFC2199) - **OPTIONAL**: no warning if missing (meaning MAY as per RFC2199) -Ultimately, through using Boutiques to define tools and their parameters, the -goal is that each tool can be interacted with as follows: +Ultimately, through using Boutiques to define tools and their parameters, +the goal is that each tool can be interacted with as follows: ```bash $ # Using Boutiques directly, the "exec launch" commands will run the app @@ -28,6 +28,6 @@ $ bids-launch bids-app --input-dataset /path/to/bids /path/to/derivatives \ --random-seed 0xBID5CAFE ``` -In the next sections, the `bids-app` tool, a Boutiques descriptor, and the -`input_params.json`, a set of invocation parameters corresponding to this app, +In the next sections, the `bids-app` tool, a Boutiques descriptor, +and the `input_params.json`, a set of invocation parameters corresponding to this app, will be defined.