From 614b81197cef13ad0c03cce41b5748f210362f7c Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Tue, 1 Dec 2020 14:49:59 -0500 Subject: [PATCH] [ENH] BEP001 - Entity-linked file collections (#688) * Squashed commit of the following: commit 8e1ac5fe358691f34ca1c2b57b5812d2dc602173 Author: Stefan Appelhoff Date: Fri Nov 27 11:09:24 2020 +0100 fix links and latin commit 27c9b41b1d1cedc38654db39b3fd5e573b8ce660 Author: Stefan Appelhoff Date: Fri Nov 27 10:03:51 2020 +0100 remove latin Co-authored-by: Chris Markiewicz commit 7d87070ecb6eb3636d5b15e304b8e65de2b8c93b Author: Agah Date: Mon Nov 23 08:46:47 2020 -0500 Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz commit b137a9e3cd2bce7cfe7853909684267d4689b692 Author: Agah Date: Mon Nov 23 08:45:19 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz commit d7897b8259213dd1cfb6e1db4ec835116491bfb1 Author: Agah Date: Mon Nov 23 08:44:40 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz commit 09e9d32b033a076a8eeb8408d5e62798bb3629ed Author: Agah Date: Mon Nov 23 08:44:15 2020 -0500 Commit suggestion Co-authored-by: Chris Markiewicz commit 009a9ab1563020c130553253480ef76467d894c2 Author: Agah Karakuzu Date: Mon Nov 23 08:43:00 2020 -0500 Add file-collecitons appendix to the TOC commit 8f6c4dfbe7f79232cadca72f0fd22b693a238c52 Author: Agah Karakuzu Date: Mon Nov 23 08:41:13 2020 -0500 Address suggestion by @tsalo commit 45210a9d167a7532c1ab8463c62dbbc519969c95 Author: Agah Karakuzu Date: Wed Nov 11 14:32:20 2020 -0500 Wording commit 66ba5a5313d4951c826063de13da2d60363b6edd Author: Agah Karakuzu Date: Wed Nov 11 14:31:40 2020 -0500 RECOMMENDED --> MUST for adding an application def to the appdx commit 5611fac6a365eef07acf36290cbf12f22a1d4751 Author: Agah Karakuzu Date: Wed Nov 11 14:29:21 2020 -0500 Improve the appendix commit 6d3bbeadc464ec4a93f97d96d3cffdad8f920f29 Author: Agah Karakuzu Date: Mon Nov 2 16:12:04 2020 -0500 Address suggestions by @tsalo commit bcb02232ca769f14a11eb8b056bb963591901012 Author: Agah Karakuzu Date: Tue Oct 27 21:37:26 2020 -0400 [ADD] Link to the appendix commit 44e760f69163eb11bec74be58279bd260aad963c Author: Agah Karakuzu Date: Tue Oct 27 21:28:38 2020 -0400 [ADD] Appendix - File collections - For parametrically linked file collections commit 523b1c163df4b5a1d46f25156d1b0ea0d06ac7bb Author: Agah Karakuzu Date: Tue Oct 27 21:27:52 2020 -0400 [ADD] Parametrically linked file collections - Description * ENH: Link to all BEP-001 entities * STY: Escape asterisk, adjust table widths * Add suggestions by @sappelhoff * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Thank you @effigies! Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz Co-authored-by: Agah Karakuzu --- mkdocs.yml | 1 + src/02-common-principles.md | 22 +++++++++++ src/99-appendices/10-file-collections.md | 47 ++++++++++++++++++++++++ 3 files changed, 70 insertions(+) create mode 100644 src/99-appendices/10-file-collections.md diff --git a/mkdocs.yml b/mkdocs.yml index 65466633d6..4fce5fb957 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -49,6 +49,7 @@ nav: - MEG systems: 99-appendices/07-meg-systems.md - Coordinate systems: 99-appendices/08-coordinate-systems.md - Entities: 99-appendices/09-entities.md + - File collections: 99-appendices/10-file-collections.md - Changelog: CHANGES.md - The BIDS Starter Kit: - GitHub repository: https://github.com/bids-standard/bids-starter-kit diff --git a/src/02-common-principles.md b/src/02-common-principles.md index f090efd094..1eadbe98e1 100644 --- a/src/02-common-principles.md +++ b/src/02-common-principles.md @@ -161,6 +161,28 @@ A summary of all entities in BIDS and the order in which they MUST be specified is available in the [entity table](./99-appendices/04-entity-table.md) in the appendix. +### Entity-linked file collections + +An entity-linked file collection is a set of files that are related to each other +based on a repetitive acquisition of sequential data +by changing acquisition parameters one (or multiple) at a time +or by being inherent components of the same data. +Entity-linked collections are identified by a common suffix, +indicating the group of files that should be considered a logical unit. +Within each collection, files MUST be distinguished from each other by at least one +entity (for example, `echo`) that corresponds to an altered acquisition parameter +(`EchoTime`) or that defines a component relationship (for example, `part`). +Note that these entities MUST be described by the specification and +the parameter changes they declare MUST NOT invalidate the definition of the accompanying suffix. +For example, the use of the `echo` entity along with the `T1w` suffix casts doubt on +the validity of the identified contrast weighting. +Provided the conditions above are satisfied, +any suffix (such as `bold`) can identify an entity-linked file collection, +although certain suffixes are exclusive for this purpose (for example, `MP2RAGE`). +Use cases concerning this convention are compiled in the +[file collections](./99-appendices/10-file-collections.md) appendix. +This convention is mainly intended for but not limited to MRI modalities. + ## Source vs. raw vs. derived data BIDS was originally designed to describe and apply consistent naming conventions diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md new file mode 100644 index 0000000000..e4517a5a28 --- /dev/null +++ b/src/99-appendices/10-file-collections.md @@ -0,0 +1,47 @@ +# Appendix X: File collections + +To give context to the use of [entity-linked file collections](../02-common-principles.md#file-name-structure), +applications concerned with this common principle are listed by descriptive tables +under their respective modalities. + +Note that the tables in this appendix catalog applications where the use of +a file collection is REQUIRED. + +Certain entitites interlink the files in a file collection through a metadata field. +Unlike other common entities (for example `run`), they require an iteration over different +values of the metadata fields they represent. +Please keep the following list of linking entities up-to-date with the file collections +included in this appendix: + +* Magnetic Resonance Imaging + * [`echo`](./09-entities.md#echo) + * [`flip`](./09-entities.md#flip) + * [`inv`](./09-entities.md#inv) + * [`mt`](./09-entities.md#mt) + * [`part`](./09-entities.md#part) + +## Magnetic Resonance Imaging + +### Anatomy imaging data + +| Suffix | Linking entities | Application | Description | +|---------|-----------------------|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| VFA | flip | Variable flip angle | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.20314)). | +| IRT1 | inv, part | Inversion recovery T1 mapping | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22497)). | +| MP2RAGE | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://www.sciencedirect.com/science/article/pii/S1053811909010738?casa_token=u_CYBx4hi7IAAAAA:3w0cMTyU5jA1BdFs0s5oVcQeqF2tZho0iJ9d4N1kExfaX27v9-JnWacF6mbEp_lMKZ64CvoTl8k) | +| MESE | echo | Multi-echo spin-echo | The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout. | +| MEGRE | echo | Multi-echo gradient-echo | Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout. | +| MTR | mt | Magnetization transfer ratio | This method is to calculate a semi-quantitative magnetization transfer ratio map. | +| MTS | flip, mt | Magnetization transfer saturation | This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle ([Helms et al. 2008](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.21732)). | +| MPM | flip, mt, echo, part | Multi-parametric mapping | The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts ([Weiskopf et al. 2013](https://www.frontiersin.org/articles/10.3389/fnins.2013.00095/full)). See [here](https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) for suggested MPM acquisition protocols. | + +### Fieldmap data + +| Suffix | Meta-data relevant entity | Application | Description | +|--------|--------------------------------|------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| TB1DAM | flip | Double-angle B1+ mapping | The double-angle B1+ method ([Insko and Bolinger 1993](https://www.sciencedirect.com/science/article/abs/pii/S1064185883711332)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging. | +| TB1EPI | flip, echo | B1+ mapping with 3D EPI | This B1+ mapping method ([Jiru and Klose 2006](https://dx.doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle. | +| TB1AFI | flip, inv | Actual Flip Angle Imaging (AFI) | This method ([Yarnykh 2007](https://dx.doi.org/10.1002/mrm.21120)) calculates a B1+ map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence | +| TB1TFL | Please see the qMRI appendix | Siemens `tfl_b1_map` | B1+ data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.22423). The sequence generates one ~anatomical image and one scaled flip angle map. | +| TB1RMF | Please see the qMRI appendix | Siemens `rf_map` | B1+ data acquired using `rf_map` product sequence by Siemens | +| RB1COR | Please see the qMRI appendix | B1- field correction | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://onlinelibrary.wiley.com/doi/full/10.1002/mrm.26058) |