From 8ccc10de35ef1906a1e38ddbb84b67a9fdbcc42d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 17 Mar 2023 10:47:26 -0400 Subject: [PATCH 1/4] Add explicit wording on DICOM terms correspondence --- src/common-principles.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/common-principles.md b/src/common-principles.md index 1b8c09a407..540bfd7f48 100644 --- a/src/common-principles.md +++ b/src/common-principles.md @@ -422,6 +422,9 @@ possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). +Many of such metadata entries are explicitly formalized in BIDS and could be found listed in the [Glossary](./glossary.md). +Whenever formalizing a new metadata entry within BIDS, the name SHOULD correspond to original DICOM Tag whenever the value is taken *as is* without any further harmonization. +The description of the term in the schema SHOULD describe such correspondence as "Corresponds to DICOM Tag ID1, ID2 `DICOM Tag Name`.". Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix) and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii) DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator) From a3e32b1422cf2238b2c491e22e374d3e57e926e8 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Sun, 31 Mar 2024 08:13:59 -0400 Subject: [PATCH 2/4] Extend to Based on for DICOM --- src/common-principles.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/common-principles.md b/src/common-principles.md index 540bfd7f48..dea781297d 100644 --- a/src/common-principles.md +++ b/src/common-principles.md @@ -423,8 +423,9 @@ acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). Many of such metadata entries are explicitly formalized in BIDS and could be found listed in the [Glossary](./glossary.md). -Whenever formalizing a new metadata entry within BIDS, the name SHOULD correspond to original DICOM Tag whenever the value is taken *as is* without any further harmonization. -The description of the term in the schema SHOULD describe such correspondence as "Corresponds to DICOM Tag ID1, ID2 `DICOM Tag Name`.". +Whenever formalizing a new metadata entry within BIDS, the name SHOULD correspond to the original DICOM Tag whenever the value is taken *as is* without any further harmonization. +The description of the term in the schema then SHOULD describe such correspondence as "Corresponds to DICOM Tag ID1, ID2 `DICOM Tag Name`.". +If value is harmonized, the description SHOULD describe such correspondence as "Based on DICOM Tag ID1, ID2 `DICOM Tag Name`.". Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix) and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii) DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator) From db081068ae62251ac88188de3c73766a2f0ab090 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Mon, 15 Apr 2024 10:36:18 +0200 Subject: [PATCH 3/4] Update src/common-principles.md Co-authored-by: Stefan Appelhoff --- src/common-principles.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/common-principles.md b/src/common-principles.md index dea781297d..f6414068d1 100644 --- a/src/common-principles.md +++ b/src/common-principles.md @@ -422,7 +422,7 @@ possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). -Many of such metadata entries are explicitly formalized in BIDS and could be found listed in the [Glossary](./glossary.md). +Many of such metadata entries are explicitly formalized in BIDS and can be found listed in the [Glossary](./glossary.md). Whenever formalizing a new metadata entry within BIDS, the name SHOULD correspond to the original DICOM Tag whenever the value is taken *as is* without any further harmonization. The description of the term in the schema then SHOULD describe such correspondence as "Corresponds to DICOM Tag ID1, ID2 `DICOM Tag Name`.". If value is harmonized, the description SHOULD describe such correspondence as "Based on DICOM Tag ID1, ID2 `DICOM Tag Name`.". From 49f686afc50adc310bedf401bcae178ab420ebcf Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Thu, 25 Apr 2024 11:43:18 -0400 Subject: [PATCH 4/4] Update avoiding "instructions to spec authors" language Co-authored-by: Chris Markiewicz --- src/common-principles.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/common-principles.md b/src/common-principles.md index f6414068d1..375496111e 100644 --- a/src/common-principles.md +++ b/src/common-principles.md @@ -422,10 +422,11 @@ possible. Since the NIfTI standard offers limited support for the various image acquisition parameters available in DICOM files, we RECOMMEND that users provide additional meta information extracted from DICOM files in a sidecar JSON file (with the same filename as the `.nii[.gz]` file, but with a `.json` extension). -Many of such metadata entries are explicitly formalized in BIDS and can be found listed in the [Glossary](./glossary.md). -Whenever formalizing a new metadata entry within BIDS, the name SHOULD correspond to the original DICOM Tag whenever the value is taken *as is* without any further harmonization. -The description of the term in the schema then SHOULD describe such correspondence as "Corresponds to DICOM Tag ID1, ID2 `DICOM Tag Name`.". -If value is harmonized, the description SHOULD describe such correspondence as "Based on DICOM Tag ID1, ID2 `DICOM Tag Name`.". +Currently defined metadata fields are listed in the [Glossary](./glossary.md). +Where possible, DICOM Tags are adopted directly as BIDS metadata terms and +indicated with "**Corresponds to** DICOM Tag ID1, ID2 `DICOM Tag Name`.". +When harmonization has been deemed necessary, this is indicated in the +BIDS term description with "**Based on** DICOM Tag ID1, ID2 `DICOM Tag Name`.". Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix) and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii) DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator)