[ENH] BEP001 - qMRI maps and some additional metadata (#690)

* Edit non-param table, add legacy list

* Add table for parametric maps

* Add description for parametric maps.

* Add templates for file collections

* Typo, wording for NumberShots

* Add spoiling metadata

* Update entity schema src

* split

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

* Wording

* a.u. --> arbitrary

* legacy --> deprecated

* mod --> label

* ADD explanations about fundamental contrasts

* Drop part from qMaps

* update entity table

* STY: Use .md links, fix table formatting

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* [ADD] qMRI Appendix

* ADD SA2RAGE and qMRI appendix links

* Entity and entity tables

- Avoid conflict with #692 
- Add applicable TB1map file collections

* ADD MixingTime & Improve NumberShots

* Consistency

* Address comment

* map units

* Super minot textual edits

* Some small textual fixes in 10-file-collections

* re-render entity table after rebase

using  python tools/bids_schema.py entities src/schema/ src/99-appendices/04-entity-table.md

* fix call to use entitytable, not entities

* fix 09-entities using correct schema call

* Drop latin phrases

* Fix double quotes

* Codeblock type fix

* Fix article hyperlinks --> DOI

* Punctuation fixes

* Add section links iof italics

* Drop etc.

* Rm Latin phrase

* add missing newline at end of file

* major syntax+linebreak overhaul qmri appendix

* remaining qmri appendix syntax issues, except one to be discussed

* fix table pipes in 10-file-collections.md

* fix ill-formatted links

* some more link fixes

* one more link

* Fix typo

* Fix parantheses

* Make spoiling-relevant requirements more explicit

* Wording suggestion

* Add unit for MixingTime

* Fix typo

* Define R1,R2,R2star and re-arrange rows

* Fix double quotes

* Fix typo

* Wording suggestion

* Rm verbosity

* Wording fix

* Number of shots array/number explanation

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/11-qmri.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* fix links by converting to lowercase

* STY: Align table fences

* STY: Fix link syntax, one more table fence

* Fix typo

* Fix paranthesis

* STY: Align table fences

* Move UNIT1 to non-parametric table

* Fix typo

* Fix typo

* Drop the term grayscale

* Align table fence

* STY: Align table fences

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Gilles de Hollander <Gilles.de.Hollander@gmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

mkdocs.yml

@@ -50,6 +50,7 @@ nav:
         - Coordinate systems: 99-appendices/08-coordinate-systems.md
         - Entities: 99-appendices/09-entities.md
         - File collections: 99-appendices/10-file-collections.md
+        - Quantitative MRI: 99-appendices/11-qmri.md
       - Changelog: CHANGES.md
     - The BIDS Starter Kit:
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit

src/schema/datatypes/anat.yaml

@@ -3,17 +3,12 @@
 - suffixes:
     - T1w
     - T2w
-    - T1rho
-    - T1map
-    - T2map
-    - T2star
+    - PDw
+    - T2starw
     - FLAIR
-    - FLASH
-    - PD
-    - PDmap
-    - PDT2
     - inplaneT1
     - inplaneT2
+    - PDT2
     - angio
   extensions:
     - .nii.gz
@@ -28,6 +23,38 @@
     rec: optional
     part: optional
 # Second group
+- suffixes:
+    - T1map
+    - T2map
+    - T2starmap
+    - R1map
+    - R2map
+    - R2starmap
+    - PDmap
+    - MTRmap
+    - MTsat
+    - UNIT1
+    - T1rho
+    - MWFmap
+    - MTVmap
+    - PDT2map
+    - Chimap
+    - TB1map
+    - RB1map
+    - S0map
+    - M0map
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+# Third group
 - suffixes:
     - defacemask
   extensions:
@@ -42,3 +69,105 @@
     ce: optional
     rec: optional
     mod: optional
+# Fourth group
+- suffixes:
+    - MESE
+    - MEGRE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: required
+    part: optional
+# Fifth group
+- suffixes:
+    - VFA
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    flip: required
+    part: optional
+# Sixth group
+- suffixes:
+    - IRT1
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    inv: required
+    part: optional
+# Seventh group
+- suffixes:
+    - MP2RAGE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: optional
+    flip: required
+    inv: required
+    part: optional
+# Eighth group
+- suffixes:
+    - MPM
+    - MTS
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: optional
+    flip: required
+    mt: required
+    part: optional
+# Nineth group
+- suffixes:
+    - MTR
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    mt: required
+    part: optional

src/schema/datatypes/fmap.yaml

@@ -31,3 +31,36 @@
     ce: optional
     dir: required
     run: optional
+# Third group
+- suffixes:
+    - TB1DAM
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    flip: required
+    part: optional
+# Fourth group
+- suffixes:
+    - TB1EPI
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    sub: required
+    ses: optional
+    run: optional
+    acq: optional
+    ce: optional
+    rec: optional
+    echo: required
+    flip: required
+    part: optional