From 78a8a66569814203f9dca949fb95b5559d1ae82e Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Sun, 6 Jun 2021 10:11:08 +0200 Subject: [PATCH 1/2] fix: inconsistency in ieeg table and text --- .../02-magnetoencephalography.md | 6 +++--- .../03-electroencephalography.md | 6 ++---- .../04-intracranial-electroencephalography.md | 7 +++---- 3 files changed, 8 insertions(+), 11 deletions(-) diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index 9fae2f7c82..ceb09e8b28 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -197,7 +197,7 @@ Missing values MUST be indicated with `n/a`. The columns of the Channels description table stored in `*_channels.tsv` are: -MUST be present: +MUST be present **in this specific order**: | **Column name** | **Requirement level** | **Description** | | --------------- | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | @@ -221,8 +221,8 @@ SHOULD be present: Example: ```Text -name type units description sampling_frequency low_cutoff high_cutoff notch software_filters status -UDIO001 TRIG V analogue trigger 1200 0.1 300 0 n/a good +name type units description sampling_frequency low_cutoff high_cutoff notch software_filters status +UDIO001 TRIG V analogue trigger 1200 0.1 300 0 n/a good MLC11 MEGGRADAXIAL T sensor 1st-order grad 1200 0 n/a 50 SSS bad ``` diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index d220f81fce..7369097bb5 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -188,8 +188,6 @@ Date time information MUST be expressed as indicated in [Units](../02-common-pri This file is RECOMMENDED as it provides easily searchable information across BIDS datasets for for example, general curation, response to queries or batch analysis. -The required columns are channel `name`, `type` and `units` in this specific -order. To avoid confusion, the channels SHOULD be listed in the order they appear in the EEG data file. Any number of additional columns may be added to provide additional information @@ -205,7 +203,7 @@ See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in The columns of the Channels description table stored in `*_channels.tsv` are: -MUST be present: +MUST be present **in this specific order**: | **Column name** | **Requirement level** | **Description** | | --------------- | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | @@ -277,7 +275,7 @@ expected in cartesian coordinates according to the `EEGCoordinateSystem` and file MUST be specified as well**. The order of the required columns in the `*_electrodes.tsv` file MUST be as listed below. -MUST be present: +MUST be present **in this specific order**: | **Column name** | **Requirement level** | **Description** | | --------------- | --------------------- | ----------------------------------- | diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index 5cf4476210..728243d077 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -203,7 +203,6 @@ Although this information can often be extracted from the iEEG recording, listing it in a simple `.tsv` document makes it easy to browse or search (for example, searching for recordings with a sampling frequency of >=1000 Hz). Hence, the channels.tsv is RECOMMENDED. -The two required columns are channel `name` and `type`. Channels SHOULD appear in the table in the same order they do in the iEEG data file. Any number of additional columns may be provided to provide additional @@ -213,7 +212,7 @@ Note that electrode positions SHOULD NOT be added to this file but to The columns of the Channels description table stored in `*_channels.tsv` are: -MUST be present: +MUST be present **in this specific order**: | **Column name** | **Requirement level** | **Description** | | --------------- | --------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | @@ -275,7 +274,7 @@ Note that upper-case is REQUIRED: Example of free-form text for field `description`: -- intracranial, stimulus, response, vertical EOG, skin conductance +- intracranial, stimulus, response, vertical EOG, skin conductance ## Electrode description (`*_electrodes.tsv`) @@ -315,7 +314,7 @@ For example: The order of the required columns in the `*_electrodes.tsv` file MUST be as listed below. -MUST be present: +MUST be present **in this specific order**: | **Column name** | **Requirement level** | **Description** | | --------------- | --------------------- | -------------------------------------------------------------------------------------------------------------------------------- | From c1c3d89b083607b1e8db962cc7b8f0e56f21c108 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Thu, 10 Jun 2021 12:41:31 +0200 Subject: [PATCH 2/2] PET: clarify that time column must be first in blood tsv --- .../09-positron-emission-tomography.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/04-modality-specific-files/09-positron-emission-tomography.md b/src/04-modality-specific-files/09-positron-emission-tomography.md index 9530103a79..bad30e4165 100644 --- a/src/04-modality-specific-files/09-positron-emission-tomography.md +++ b/src/04-modality-specific-files/09-positron-emission-tomography.md @@ -332,7 +332,8 @@ The following metadata SHOULD or MUST be provided if corresponding flags are `tr | MetaboliteMethod | REQUIRED if `MetaboliteAvail` is `true` | [string][] | Method used to measure metabolites. | | MetaboliteRecoveryCorrectionApplied | REQUIRED if `MetaboliteAvail` is `true` | [boolean][] | Metabolite recovery correction from the HPLC, for tracers where it changes with time postinjection. If `true`, the `hplc_recovery_fractions` column MUST be present in the corresponding `*_blood.tsv` file. | -The following columns are defined for `_blood.tsv` files: +The following columns are defined for `_blood.tsv` files. +The `time` column MUST always be the first column. | **Column name** | **Requirement level** | **Description** | **Units** | | ---------------------------- | ----------------------------------------------------------- | --------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- |