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Allow IntendedFor and make task- optional for _sbref.ext #47

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oesteban opened this issue Jul 3, 2019 · 0 comments
Open

Allow IntendedFor and make task- optional for _sbref.ext #47

oesteban opened this issue Jul 3, 2019 · 0 comments

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@oesteban
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oesteban commented Jul 3, 2019

Related to bids-standard/bids-specification#239.

Some fMRI studies will not acquire one SBRef for every multiband BOLD scan (this is probably true for DWI too, and thus bids-standard/bids-specification#239).

Currently, the task-Name entity needs to be defined for SBRefs. Doing it optional, would allow the following:

func/
  sub-3010_sbref.nii.gz
  sub-3010_task-discountFix_run-1_bold.nii.gz
  sub-3010_task-manipulationTask_run-1_bold.nii.gz
  sub-3010_task-motorSelectiveStop_run-1_bold.nii.gz
  sub-3010_task-rest_run-1_bold.nii.gz
  sub-3010_task-rest_run-1_sbref.nii.gz
  sub-3010_task-stopSignal_run-1_bold.nii.gz

Where, by the inheritance principle, sub-3010_sbref.nii.gz is intended for all tasks but rest because a particular sbref exists for that one.

Additionally, I propose to allow defining the IntendedFor metadata for SBRefs, so the same behavior can be implemented without missing the provenance about what task was acquired closest to the sbref, e.g.:

func/
  sub-3010_task-discountFix_run-1_bold.nii.gz
  sub-3010_task-discountFix_run-1_sbref.json
  sub-3010_task-discountFix_run-1_sbref.nii.gz
  sub-3010_task-manipulationTask_run-1_bold.nii.gz
  sub-3010_task-motorSelectiveStop_run-1_bold.nii.gz
  sub-3010_task-rest_run-1_bold.nii.gz
  sub-3010_task-rest_run-1_sbref.nii.gz
  sub-3010_task-stopSignal_run-1_bold.nii.gz

where sub-3010_task-discountFix_run-1_sbref.json has an IntendedFor field:

{
  "IntendedFor": [
    "sub-3010_task-discountFix_run-1_bold.nii.gz",
    "sub-3010_task-manipulationTask_run-1_bold.nii.gz",
    "sub-3010_task-motorSelectiveStop_run-1_bold.nii.gz",
    "sub-3010_task-stopSignal_run-1_bold.nii.gz"
  ]
}
oesteban referenced this issue in oesteban/bids-specification Sep 28, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 23, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 23, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 26, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 26, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 28, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Oct 28, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
oesteban referenced this issue in oesteban/bids-specification Nov 6, 2020
This PR addresses the problem @mattcieslak spotted at in bids-standard#239.

This enhancement (WIP) basically allows for researchers to encode
the protocol's intent regarding fieldmaps.

As @satra introduced in bids-standard#239 (comment),
BIDS "*could encode intent and automation. Whether it should is a community decision."

This PR proposes a solution to encoding the intent. It doesn't modify
anything to allow also encoding automation.

The PR attempts to be backwards compatible, and is based off of bids-standard#651,
where the text about fieldmaps is being revised.

I'm submitting this draft PR to open discussions and looking forward to
feedback.

Resolves: bids-standard#239.
Depends: bids-standard#651.
References: #263, nipreps/dmriprep#43, bids-standard/bids-2-devel#39
@Remi-Gau Remi-Gau transferred this issue from bids-standard/bids-specification Feb 22, 2021
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