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[FIX] fix inconsistencies for task label between sections #446

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Apr 17, 2020
Merged

[FIX] fix inconsistencies for task label between sections #446

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45f92ea
uniformize task label for beh and ieeg
Remi-Gau Apr 14, 2020
8e0a141
fix typo and add markup in beh
Remi-Gau Apr 14, 2020
ad935c2
fix typo in ieeg
Remi-Gau Apr 14, 2020
126ae34
make all task label description match that of fMRI
Remi-Gau Apr 14, 2020
42bcc6c
Improve TaskName field descriptions in all sections
Remi-Gau Apr 14, 2020
fdf5cfd
fix missing hyphen and change TaskName description in MRI section
Remi-Gau Apr 15, 2020
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4 changes: 2 additions & 2 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -273,10 +273,10 @@ JSON file.
#### Required fields

| Field name | Definition |
|-----------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| RepetitionTime | REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. |
| VolumeTiming | REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined. |
| TaskName | REQUIRED. Name of the task. No two tasks should have the same name. Task label (`task-`) included in the file name is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. For example task name `faces n-back` will corresponds to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`. |
| TaskName | REQUIRED. Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`. |

For the fields described above and in the following section, the term "Volume"
refers to a reconstruction of the object being imaged (e.g., brain or part of a
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6 changes: 3 additions & 3 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -59,9 +59,9 @@ actually be exploited.

Generic fields MUST be present:

| Field name | Definition |
| ---------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| TaskName | REQUIRED. Name of the task (for resting state use the `rest` prefix). Different Tasks SHOULD NOT have the same name. The Task label is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. |
| Field name | Definition |
|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| TaskName | REQUIRED. Name of the task (for resting state use the `rest` prefix). No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. |

SHOULD be present: For consistency between studies and institutions, we
encourage users to extract the values of these fields from the actual raw data.
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6 changes: 3 additions & 3 deletions src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -89,9 +89,9 @@ be specified.

Generic fields MUST be present:

| Field name | Definition |
| --------------------------------------------------------------------------------------| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| TaskName | REQUIRED. Name of the task (for resting state use the `rest` prefix). Different Tasks SHOULD NOT have the same name. The Task label is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. |
| Field name | Definition |
|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| TaskName | REQUIRED. Name of the task (for resting state use the `rest` prefix). No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. |

SHOULD be present: For consistency between studies and institutions, we
encourage users to extract the values of these fields from the actual raw data.
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12 changes: 6 additions & 6 deletions src/04-modality-specific-files/04-intracranial-electroencephalography.md
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Expand Up @@ -23,8 +23,8 @@ Template:
sub-<label>/
[ses-<label>]/
ieeg/
sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.<manufacturer_specific_extension>
sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_ieeg.<manufacturer_specific_extension>
sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_ieeg.json
```

The iEEG community uses a variety of formats for storing raw data, and there is
Expand Down Expand Up @@ -70,7 +70,7 @@ Note the RecordingType, which depends on whether the data stream on disk is inte
### Terminology: Electrodes vs. Channels

For proper documentation of iEEG recording metadata it is important to
understand the difference between electrode and channel: An iEEG electrode
understand the difference between electrode and channel: an iEEG electrode
is placed on or in the brain, whereas a channel is the combination of the analog
differential amplifier and analog-to-digital converter that result in a
potential (voltage) difference that is stored in the iEEG dataset. We employ the
Expand Down Expand Up @@ -102,9 +102,9 @@ please avoid using ad hoc wording.

Generic fields MUST be present:

| Field name | Definition |
| --------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| TaskName | REQUIRED. Name of the task (for resting state use the "rest" prefix). No two tasks should have the same name. Task label is derived from this field by removing all non alphanumeric (`[a-zA-Z0-9]`) characters. Note this does not have to be a "behavioral task" that subjects perform, but can reflect some information about the conditions present when the data was acquired (e.g., "rest", "sleep", or "seizure"). |
| Field name | Definition |
|------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| TaskName | REQUIRED. Name of the task (for resting state use the "rest" prefix). No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. Note this does not have to be a "behavioral task" that subjects perform, but can reflect some information about the conditions present when the data was acquired (e.g., "rest", "sleep", or "seizure"). |

SHOULD be present: For consistency between studies and institutions, we
encourage users to extract the values of these fields from the actual raw data.
Expand Down
20 changes: 10 additions & 10 deletions src/04-modality-specific-files/07-behavioral-experiments.md
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Expand Up @@ -5,22 +5,22 @@ Template:
```Text
sub-<label>/[ses-<label>/]
beh/
sub-<label>[_ses-<label>]_task-<task_name>_events.tsv
sub-<label>[_ses-<label>]_task-<task_name>_events.json
sub-<label>[_ses-<label>]_task-<task_name>_beh.tsv
sub-<label>[_ses-<label>]_task-<task_name>_beh.json
sub-<label>[_ses-<label>]_task-<task_name>_physio.tsv.gz
sub-<label>[_ses-<label>]_task-<task_name>_physio.json
sub-<label>[_ses-<label>]_task-<task_name>_stim.tsv.gz
sub-<label>[_ses-<label>]_task-<task_name>_stim.json
sub-<label>[_ses-<label>]_task-<label>_events.tsv
sub-<label>[_ses-<label>]_task-<label>_events.json
sub-<label>[_ses-<label>]_task-<label>_beh.tsv
sub-<label>[_ses-<label>]_task-<label>_beh.json
sub-<label>[_ses-<label>]_task-<label>_physio.tsv.gz
sub-<label>[_ses-<label>]_task-<label>_physio.json
sub-<label>[_ses-<label>]_task-<label>_stim.tsv.gz
sub-<label>[_ses-<label>]_task-<label>_stim.json
```

In addition to logs from behavioral experiments performed along imaging data
acquisitions one can also include data from experiments performed outside of the
scanner. The results of those experiments can be stored in the beh folder using
scanner. The results of those experiments can be stored in the `beh` folder using
the same formats for event timing (`_events.tsv`), metadata (`_events.json`),
physiological (`_physio.tsv.gz`, `_physio.json`) and other continuous recordings
(`_stim.tsv.gz`, `_stim.json`) as for tasks performed during MRI acquisitions.
Additionally, events files that do not include the mandatory `onset` and
`duration` columns can still be included, but should be labelled `_beh.tsv`
`duration` columns can still be included, but should be labeled `_beh.tsv`
rather than `_events.tsv`.