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[ENH] Add FA images #1831

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[ENH] Add FA images #1831

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e5d9e04
add FA
CPernet May 23, 2024
691e73d
FA suffix
CPernet May 23, 2024
45c14fd
add FA
CPernet May 23, 2024
2e4627e
Update src/schema/rules/files/raw/dwi.yaml
CPernet May 27, 2024
4040942
Update src/modality-specific-files/magnetic-resonance-imaging-data.md
CPernet May 27, 2024
0b3a498
add colFA
CPernet May 27, 2024
f28e539
add colFA
CPernet May 27, 2024
74220cf
colFA description
CPernet May 27, 2024
12b780e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 27, 2024
081a59f
fix(schema): Rename raw reference in derivative rules
effigies May 29, 2024
b78b033
Update src/modality-specific-files/magnetic-resonance-imaging-data.md
CPernet Jun 21, 2024
583acd1
Update src/modality-specific-files/magnetic-resonance-imaging-data.md
CPernet Jun 21, 2024
5cabca0
Update src/schema/objects/suffixes.yaml
CPernet Jun 21, 2024
2dd88b6
Merge branch 'master' into add-FA-images
CPernet Jun 28, 2024
ac7584e
all lower case
CPernet Jun 28, 2024
3e991a5
all lower case
CPernet Jun 28, 2024
7c492c2
scanner deriv as lower case.yaml
CPernet Jun 28, 2024
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8 changes: 4 additions & 4 deletions src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -667,7 +667,7 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_suffix_table(["ADC", "TRACE"]) }}
{{ MACROS___make_suffix_table(["adc", "trace", "fa", "colfa"]) }}

<!--
This block generates a filename templates.
Expand Down Expand Up @@ -696,9 +696,9 @@ In such a case, two files could have the following names:
The user is free to choose any other label than `singleband` and
`multiband`, as long as they are consistent across subjects and sessions.

Scanner-generated TRACE and ADC volumes MAY be included using the
`TRACE` and `ADC` suffixes.
If TRACE or ADC volume filenames match a diffusion series with all applicable entities,
Scanner-generated trace, ADC and fractional anisotropy (fa and colfa) volumes MAY be included
using the `trace`, `adc`, `fa` and `colfa` suffixes, respectively.
If trace, adc, fa, or colfa volume filenames match a diffusion series with all applicable entities,
such volumes SHOULD be computed from that series.
Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
SHOULD be used to indicate that the files are unrelated.
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20 changes: 16 additions & 4 deletions src/schema/objects/suffixes.yaml
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Expand Up @@ -6,8 +6,8 @@ TwoPE:
display_name: 2-photon excitation microscopy
description: |
2-photon excitation microscopy imaging data
ADC:
value: ADC
adc:
value: adc
display_name: Apparent diffusion coefficient (ADC)
description:
Apparent diffusion coefficient (ADC) map
Expand Down Expand Up @@ -42,11 +42,23 @@ DIC:
display_name: Differential interference contrast microscopy
description: |
Differential interference contrast microscopy imaging data
colfa:
value: colfa
display_name: Colored Fractional Anisotropy image
description: |
Diffusion images reflecting the directionality of the diffusion tensor color-coded in red for
left-right oriented fibers, in blue for superior-inferior oriented fibers and green for
anterior-posterior oriented fibers.
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Sorry to chime in here. I may have missed other related discussions, but I'd dare to say that these are usually referred to as DEC (diffusion-encoded colormaps). Most commonly they contain FA information, but could be other information. They are referred to as DECFA in BEP016.

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Thx for the info! If DECFA is preferred we can just as easily use that, I have no preference but what expert people tell me we should do.

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I don't think BEP016 ever uses "DECFA" specifically. The fact that the nature of orientation encoding across volumes is directionally-encoded colour, and that the quantitative parameter encoded in the image is FA, are treated very deliberately as two separate dimensions. The distinction between scanner-generated derivatives and pipeline-generated BIDS Derivatives nevertheless means that there doesn't actually need to be correspondence between the two. Indeed a colour FA image generated by a pipeline will not use this suffix, even though the information encoded is identical.

I maybe have a slight preference for "colFA" just because it's consistent with data being emitted by many scanners that are intended to be encoded in this way.

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Thanks for the explanation.

The distinction between scanner-generated derivatives and pipeline-generated BIDS Derivatives nevertheless means that there doesn't actually need to be correspondence between the two.

Interesting. Did not know about the distinction.

Ad for the label itself, maybe I had a look at the wrong location then: the BEP016 gdocs does mention DECFA when talking about <map_label> fields on page 8: https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60/edit#heading=h.mqkmyp254xh6
Linked from:
https://bids-specification.readthedocs.io/en/v1.2.1/06-extensions.html

Maybe the google doc should not be linked from the BIDS specification website to avoid confusion?

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That BEP016 Google doc is highly outdated; development work on that project transitioned to GitHub some time ago. Maybe that should be flagged near the top of the document, and the website link should be changed. Here's the current status:
bids-standard/bids-bep016#24

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Maybe that should be flagged near the top of the document, and the website link should be changed

Done!

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👍 thanks for doing this.

DF:
value: DF
display_name: Dark-field microscopy
description: |
Dark-field microscopy imaging data
fa:
value: fa
display_name: Fractional Anisotropy image
description: |
Diffusion images reflecting the directionality of the diffusion tensor
FLAIR:
value: FLAIR
display_name: Fluid attenuated inversion recovery image
Expand Down Expand Up @@ -465,8 +477,8 @@ TEM:
display_name: Transmission electron microscopy
description: |
Transmission electron microscopy imaging data
TRACE:
value: TRACE
trace:
value: trace
display_name: Trace diffusion weighted image
description: |
Diffusion images proportional to the trace of the diffusion tensor
Expand Down
6 changes: 3 additions & 3 deletions src/schema/rules/files/deriv/imaging.yaml
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Expand Up @@ -26,10 +26,10 @@ dwi_volumetric:
density: optional
description: optional

dwi_isotropic:
$ref: rules.files.raw.dwi.isotropic
dwi_scannerderivatives:
$ref: rules.files.raw.dwi.ScannerDerivatives
entities:
$ref: rules.files.raw.dwi.isotropic.entities
$ref: rules.files.raw.dwi.ScannerDerivatives.entities
space: optional
resolution: optional
density: optional
Expand Down
8 changes: 5 additions & 3 deletions src/schema/rules/files/raw/dwi.yaml
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Expand Up @@ -40,10 +40,12 @@ sbref:
chunk: optional

# Common scanner-generated derivatives need raw names
isotropic:
ScannerDerivatives:
suffixes:
- ADC
- TRACE
- adc
- colfa
- fa
- trace
extensions:
- .nii.gz
- .nii
Expand Down