From 7ca422f9afea1171ac9ea863b02db2333c289eeb Mon Sep 17 00:00:00 2001 From: Cyril Pernet Date: Fri, 30 Jun 2023 14:43:44 +0200 Subject: [PATCH 1/9] define raw and derivatives.md follow the BIDS derivatives meeting --- src/derivatives/introduction.md | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index c18e8d5190..7c98492fd9 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -1,12 +1,19 @@ # BIDS Derivatives -Derivatives are outputs of common processing pipelines, capturing data and +Derivatives are outputs of common processing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those -outputs in subsequent processing. +outputs in subsequent processing. Standardizing derivatives is motivated by use cases where formalized -machine-readable access to processed data enables higher level processing. +machine-readable access to processed data enables higher-level processing. + +The following sections cover additions to and divergences from "raw" BIDS. Raw data are +data that have been curated to BIDS, i.e. a BIDS “raw” dataset does not have another BIDS +dataset as a source. If you are in doubt if your dataset is "raw" or +is "derivatives" ask yourself the following question: "Are my data derived from at least +one BIDS valid dataset?" if the answer is yes, then this is a BIDS derivative dataset. + +## Derivatives storage and folders structure -The following sections cover additions to and divergences from "raw" BIDS. Placement and naming conventions for derived datasets are addressed in [Storage of derived datasets][storage], and dataset-level metadata is included in [Derived dataset and pipeline description][derived-dataset-description]. From 38f40f390123a6635f111caf18a9506dd545ebd4 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 30 Jun 2023 12:47:18 +0000 Subject: [PATCH 2/9] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/derivatives/introduction.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index 7c98492fd9..7258dbbccb 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -1,16 +1,16 @@ # BIDS Derivatives -Derivatives are outputs of common processing pipelines, capturing data and +Derivatives are outputs of common processing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those -outputs in subsequent processing. +outputs in subsequent processing. Standardizing derivatives is motivated by use cases where formalized machine-readable access to processed data enables higher-level processing. -The following sections cover additions to and divergences from "raw" BIDS. Raw data are +The following sections cover additions to and divergences from "raw" BIDS. Raw data are data that have been curated to BIDS, i.e. a BIDS “raw” dataset does not have another BIDS dataset as a source. If you are in doubt if your dataset is "raw" or is "derivatives" ask yourself the following question: "Are my data derived from at least -one BIDS valid dataset?" if the answer is yes, then this is a BIDS derivative dataset. +one BIDS valid dataset?" if the answer is yes, then this is a BIDS derivative dataset. ## Derivatives storage and folders structure From 7dd3d17b440c7210755e6ac109dd5c66dc9059e9 Mon Sep 17 00:00:00 2001 From: Cyril Pernet Date: Fri, 30 Jun 2023 15:57:20 +0200 Subject: [PATCH 3/9] Update src/derivatives/introduction.md Co-authored-by: Yaroslav Halchenko --- src/derivatives/introduction.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index 7258dbbccb..c6657d21cd 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -10,7 +10,7 @@ The following sections cover additions to and divergences from "raw" BIDS. Raw d data that have been curated to BIDS, i.e. a BIDS “raw” dataset does not have another BIDS dataset as a source. If you are in doubt if your dataset is "raw" or is "derivatives" ask yourself the following question: "Are my data derived from at least -one BIDS valid dataset?" if the answer is yes, then this is a BIDS derivative dataset. +one other valid BIDS dataset?" if the answer is yes, then this is a BIDS derivative dataset. ## Derivatives storage and folders structure From 90b887480736b3e9d80ddf13d4428bac931fe10c Mon Sep 17 00:00:00 2001 From: Cyril Pernet Date: Wed, 5 Jul 2023 20:56:25 +0200 Subject: [PATCH 4/9] Update introduction.md add examples --- src/derivatives/introduction.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index c6657d21cd..a1d0895f44 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -12,6 +12,18 @@ dataset as a source. If you are in doubt if your dataset is "raw" or is "derivatives" ask yourself the following question: "Are my data derived from at least one other valid BIDS dataset?" if the answer is yes, then this is a BIDS derivative dataset. +Examples: + +A defaced T1w image would typically be made during the curation process and is thus under raw + +`sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz` +`sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` + +A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives + +`sub-01/anat/sub-01_T1w.nii.gz` +`derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` + ## Derivatives storage and folders structure Placement and naming conventions for derived datasets are addressed in From 32b6cd4b0b2441bd2c087fa6a1ba50e6cf3ea787 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 5 Jul 2023 18:56:45 +0000 Subject: [PATCH 5/9] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/derivatives/introduction.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index a1d0895f44..bcfab302c5 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -16,12 +16,12 @@ Examples: A defaced T1w image would typically be made during the curation process and is thus under raw -`sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz` +`sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz` `sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives -`sub-01/anat/sub-01_T1w.nii.gz` +`sub-01/anat/sub-01_T1w.nii.gz` `derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` ## Derivatives storage and folders structure From 64bd1c811e42524146d48b33c7e6a4b788b955f3 Mon Sep 17 00:00:00 2001 From: Cyril Pernet Date: Mon, 10 Jul 2023 14:39:38 +0200 Subject: [PATCH 6/9] Update src/derivatives/introduction.md Co-authored-by: Chris Markiewicz --- src/derivatives/introduction.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index bcfab302c5..1a2bd1189a 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -21,8 +21,10 @@ A defaced T1w image would typically be made during the curation process and is t A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives -`sub-01/anat/sub-01_T1w.nii.gz` -`derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` +``` +sub-01/anat/sub-01_T1w.nii.gz +derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz +``` ## Derivatives storage and folders structure From 583590a83863e704fcb6877d8017871cef2be578 Mon Sep 17 00:00:00 2001 From: Cyril Pernet Date: Mon, 10 Jul 2023 14:39:57 +0200 Subject: [PATCH 7/9] Update src/derivatives/introduction.md Co-authored-by: Chris Markiewicz --- src/derivatives/introduction.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index 1a2bd1189a..9b3b61dd49 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -6,11 +6,9 @@ outputs in subsequent processing. Standardizing derivatives is motivated by use cases where formalized machine-readable access to processed data enables higher-level processing. -The following sections cover additions to and divergences from "raw" BIDS. Raw data are -data that have been curated to BIDS, i.e. a BIDS “raw” dataset does not have another BIDS -dataset as a source. If you are in doubt if your dataset is "raw" or -is "derivatives" ask yourself the following question: "Are my data derived from at least -one other valid BIDS dataset?" if the answer is yes, then this is a BIDS derivative dataset. +The following sections cover additions to and divergences from "raw" BIDS. +Raw data are data that have been curated into BIDS from a non-BIDS source. +If a dataset is derived from at least one other valid BIDS dataset, then it is a derivative dataset. Examples: From 882a9d6b7767163ba3475580a02d0c8eff7f313b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 11 Jul 2023 10:30:40 -0400 Subject: [PATCH 8/9] FIX: Update code fences --- src/derivatives/introduction.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index 9b3b61dd49..a8662d67bd 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -14,12 +14,14 @@ Examples: A defaced T1w image would typically be made during the curation process and is thus under raw -`sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz` -`sub-01/anat/sub-01_desc-defaced_T1w.nii.gz` +```Text +sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz +sub-01/anat/sub-01_T1w.nii.gz +``` A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives -``` +```Text sub-01/anat/sub-01_T1w.nii.gz derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz ``` From 915aa3eb46c79f916fe992606dc6d7e8156eb334 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 11 Jul 2023 10:32:42 -0400 Subject: [PATCH 9/9] FIX: folders -> directory For consistency --- src/derivatives/introduction.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index a8662d67bd..9cad29a14a 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -26,7 +26,7 @@ sub-01/anat/sub-01_T1w.nii.gz derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz ``` -## Derivatives storage and folders structure +## Derivatives storage and directory structure Placement and naming conventions for derived datasets are addressed in [Storage of derived datasets][storage], and dataset-level metadata is included