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"Unknown" modalities are mentioned in the text #569

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yarikoptic opened this issue Aug 10, 2020 · 2 comments
Closed

"Unknown" modalities are mentioned in the text #569

yarikoptic opened this issue Aug 10, 2020 · 2 comments

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@yarikoptic
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ran into while reviewing #475 . Text refers to RARE and FLASHsubsampled although none such is listed among known modalities

$> git grep -e RARE  -e FLASHsubsampled                                    
src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md:are used to record the same modality (e.g. RARE and FLASH for T1w) this field
src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md:distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md:FLASHsubsampled) remains at the discretion of the researcher.
@effigies
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effigies commented Aug 10, 2020

These appear to be suggestions for acq- values.

#### The `acq` entity
The OPTIONAL `acq-<label>` key/value pair corresponds to a custom label the user
MAY use to distinguish a different set of parameters used for acquiring the same
modality. For example this should be used when a study includes two T1w images -
one full brain low resolution and and one restricted field of view but high
resolution. In such case two files could have the following names:
`sub-01_acq-highres_T1w.nii.gz` and `sub-01_acq-lowres_T1w.nii.gz`, however the
user is free to choose any other label than `highres` and `lowres` as long as
they are consistent across subjects and sessions. In case different sequences
are used to record the same modality (e.g. RARE and FLASH for T1w) this field
can also be used to make that distinction. At what level of detail to make the
distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and
FLASHsubsampled) remains at the discretion of the researcher.

Edit: I guess that's obvious, but I'm not sure there's an implication that these correspond to modalities as well as just sequence names, if that's what's you're supposing.

@yarikoptic
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nah, I think I just rushed into filing an issue... indeed it makes sense to annotate "peculiar" acquisitions for which we have no suffix in acq-.

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