Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[FIX] Reorganize rec, ce entities, _defacemask #550

Merged
merged 2 commits into from
Aug 8, 2020
Merged

[FIX] Reorganize rec, ce entities, _defacemask #550

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
dd2a832
Reorganize rec, ce entities, defacemask
emdupre Jul 31, 2020
b2807fb
Apply suggestions from code review
emdupre Jul 31, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 12 additions & 12 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,13 @@ modalities include:
| Inplane T2 | inplaneT2 | T2-weighted anatomical image matched to functional acquisition |
| Angiography | angio | |

If the structural images included in the dataset were defaced (to protect
identity of participants) one CAN provide the binary mask that was used to
emdupre marked this conversation as resolved.
Show resolved Hide resolved
remove facial features in the form of `_defacemask` files. In such cases the
OPTIONAL `mod-<label>` key/value pair corresponds to modality label for eg: T1w,
inplaneT1, referenced by a defacemask image. E.g.,
`sub-01_mod-T1w_defacemask.nii.gz`.
emdupre marked this conversation as resolved.
Show resolved Hide resolved

#### The `run` entity

If several scans of the same modality are acquired they MUST be indexed with a
Expand Down Expand Up @@ -168,18 +175,6 @@ sequences using different contrast enhanced images. The label is the name of the
contrast agent. The key `ContrastBolusIngredient` MAY be also be added in the
JSON file, with the same label.

#### The `rec` entity

Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
different reconstruction algorithms (for example ones using motion correction).

If the structural images included in the dataset were defaced (to protect
identity of participants) one CAN provide the binary mask that was used to
remove facial features in the form of `_defacemask` files. In such cases the
OPTIONAL `mod-<label>` key/value pair corresponds to modality label for eg: T1w,
inplaneT1, referenced by a defacemask image. E.g.,
`sub-01_mod-T1w_defacemask.nii.gz`.

Some meta information about the acquisition MAY be provided in an additional
JSON file. See [Common metadata fields](#common-metadata-fields) for a
list of terms and their definitions. There are also some OPTIONAL JSON
Expand All @@ -189,6 +184,11 @@ fields specific to anatomical scans:
| -----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------- |
| ContrastBolusIngredient | OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |

#### The `rec` entity

Similarly the OPTIONAL `rec-<label>` key/value can be used to distinguish
emdupre marked this conversation as resolved.
Show resolved Hide resolved
different reconstruction algorithms (for example ones using motion correction).

### Task (including resting state) imaging data

Currently supported image contrasts include:
Expand Down