[ENH] BEP001 - Entity-linked file collections #668
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I cannot see |
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I gave ‘me-fMRI’ just as an example application name outside the anatomy imaging. It is planned to be used with the ‘bold’ suffix with the ‘echo’ entity. Then again, this PR does not intend adding it, sorry for the confusion. One of the key reasons why file collections are introduced as a common principle is that they can be expanded for any modality by sub-communities as they see fit. |
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Cycling to re-run CI. Might need to rebase on |
| | TB1DAM | flip | Double-angle B1+ mapping | The double-angle B1<sup>+</sup> 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<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> 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<sup>+</sup> 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<sup>+</sup> 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. | |
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Do we intend to get the qMRI appendix in before the next release? Could we put in another placeholder for now, or only add these entries when the qMRI appendix is added?
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@effigies merging this PR and the new entities mentioned here adds the major components of BEP001 to the spec. I think shipping the qMRI appendix in the next release adds to the clarity of these new concepts.
To prevent link-checker fails, I did not create links. What alternative placeholder would you suggest?
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What alternative placeholder would you suggest?
I suggest that after this PR is merged you ( @agahkarakuzu ) make a new PR introducing the QMRI appendix to the spec, which you can then link to. Would that be possible relatively quickly, or do you have to prepare it first?
I remember that you said in a meeting that all of the material is basically "ready"
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okay, I just checked --> I can now successfully commit to this branch thanks to Kirstie who updated the permissions 🎉 @agahkarakuzu just a reminder to always |
Headnote
A while ago we started #508, where you can find information on the overall purpose of
BEP001. The PR #508 was closed as discussions called for some major revisions and to splitBEP001pull requests into manageable parts.Dear BIDS community,
In this Part-1 of the BEP001 pull requests, we would like to introduce a new common principle:
Entity-linked file collections.Firstly, big thanks to Taylor Salo (@tsalo) and Elizabeth DuPre (@emdupre), whose revision to the
grouping suffix(by #508) led to the development ofentity-linked file collections. We believe that this common principle is going to be of good use for many MRI applications and possibly for other imaging modalities. A summary of this discussion can be found at this comment.This enhancement introduces the convention of file collections whose individual files are distinguished using entities such as
echo,flip,mt,inv,partand that are namespaced by suffixes to define applications depending on a data acquisition with different parameters or file parts (e.g.,MP2RAGEfor T1 mapping,MPMto generate multiple quantitative maps ,ME-fMRIto provideEchoTimedependent fMRI analysis orTB1DAMto generate RF transmit field maps).In addition to a description of this proposed common principle (added as a sub-section to the
File name structuresection in02-common-principles.md), this PR includes a new appendix (10-file-collections.md) that serves as a catalog for all the applications (from any modalities) using this common principle. Please note that this appendix includes some entities (e.g.flip) and suffixes (e.g.MP2RAGE) that have not been added to the main specification yet. BEP001 will soon make PRs to introduce these suffixes and entities that currently exist as placeholders in10-file-collections.md.On behalf of the BEP001 core team:
Gilles de Hollander (@Gilles86), Alberto Lazari (@lazaral), Christophe Phillips (@ChristophePhillips), Kirstie Whitaker (@KirstieJane), Tibor Auer (@tiborauer).
Best regards.