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Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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@sappelhoff @effigies
sappelhoff and effigies committed Jun 22, 2020
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17 changes: 8 additions & 9 deletions src/02-common-principles.md
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Expand Up @@ -290,8 +290,7 @@ within that specific series directory specifying the TR for that specific run.
There is no notion of "unsetting" a key/value pair.
Once a key/value pair is set in a given level in the dataset, lower down in
the hierarchy that key/value pair will always have some assigned value.
Files for a particular
participant can exist only at participant level directory, i.e
Files for a particular participant can exist only at participant level directory, i.e
`/dataset/sub-*[/ses-*]/sub-*_T1w.json`. Similarly, any file that is not
specific to a participant is to be declared only at top level of dataset for eg:
`task-sist_bold.json` must be placed under `/dataset/task-sist_bold.json`
Expand Down Expand Up @@ -423,13 +422,13 @@ dictionary matches a column name in the TSV file, then that field MUST contain a
description of the corresponding column, using an object containing the following
fields:

| Field name | Definition |
| :---------- | :--------------------------------------------------------------------------------------------------------------------- |
| LongName | Long (unabbreviated) name of the column. |
| Description | Description of the column. |
| Levels | For categorical variables: a dictionary of possible values (keys) and their descriptions (values). |
| Units | Measurement units. SI units in CMIXF formatting are RECOMMENDED (see [units section](./02-common-principles.md#units). |
| TermURL | URL pointing to a formal definition of this type of data in an ontology available on the web. |
| Field name | Definition |
| :---------- | :-------------------------------------------------------------------------------------------------------------- |
| LongName | Long (unabbreviated) name of the column. |
| Description | Description of the column. |
| Levels | For categorical variables: a dictionary of possible values (keys) and their descriptions (values). |
| Units | Measurement units. SI units in CMIXF formatting are RECOMMENDED (see [Units](./02-common-principles.md#units)). |
| TermURL | URL pointing to a formal definition of this type of data in an ontology available on the web. |

Example:

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3 changes: 1 addition & 2 deletions src/03-modality-agnostic-files.md
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Expand Up @@ -336,8 +336,7 @@ imaging acquisition sequence (each run `.nii[.gz]` file) within one session.
Each `.nii[.gz]` file should be described by at most one row.
Relative paths to files should be used under a compulsory `filename` header.
If acquisition time is included it should be under `acq_time` header.
Datetime should be expressed as described in the
[Units section](./02-common-principles.md#units).
Datetime should be expressed as described in [Units](./02-common-principles.md#units).
For anonymization purposes all dates within one subject should be shifted by a
randomly chosen (but consistent across all runs etc.) number of days.
This way relative timing would be preserved, but chances of identifying a
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10 changes: 5 additions & 5 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -199,11 +199,11 @@ The columns of the Channels description table stored in `*_channels.tsv` are:

MUST be present:

| Column name | Definition |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name | REQUIRED. Channel name (e.g., MRT012, MEG023) |
| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [units section](../02-common-principles.md#units). |
| Column name | Definition |
| ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name | REQUIRED. Channel name (e.g., MRT012, MEG023) |
| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [Units](../02-common-principles.md#units)). |

SHOULD be present:

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10 changes: 5 additions & 5 deletions src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -214,11 +214,11 @@ The columns of the Channels description table stored in `*_channels.tsv` are:

MUST be present:

| Column name | Definition |
| ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name | REQUIRED. Channel name (e.g., FC1, Cz) |
| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [units section](../02-common-principles.md#units). |
| Column name | Definition |
| ----------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name | REQUIRED. Channel name (e.g., FC1, Cz) |
| type | REQUIRED. Type of channel; MUST use the channel types listed below. |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [Units](../02-common-principles.md#units)). |

SHOULD be present:

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2 changes: 1 addition & 1 deletion src/04-modality-specific-files/04-intracranial-electroencephalography.md
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Expand Up @@ -239,7 +239,7 @@ MUST be present:
| ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| name | REQUIRED. Label of the channel. The label must correspond to \_electrodes.tsv name and all ieeg type channels are required to have a position. The reference channel name MAY be provided in the reference column. |
| type | REQUIRED. Type of channel, see below for adequate keywords in this field. |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [units section](../02-common-principles.md#units). |
| units | REQUIRED. Physical unit of the value represented in this channel, e.g., `V` for Volt, or `fT/cm` for femto Tesla per centimeter (see [Units](../02-common-principles.md#units)). |
| low_cutoff | REQUIRED. Frequencies used for the low pass filter applied to the channel in Hz. If no low pass filter was applied, use `n/a`. Note that anti-alias is a low pass filter, specify its frequencies here if applicable. |
| high_cutoff | REQUIRED. Frequencies used for the high pass filter applied to the channel in Hz. If no high pass filter applied, use `n/a`. |

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10 changes: 5 additions & 5 deletions src/99-appendices/05-units.md
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@@ -1,6 +1,6 @@
# Appendix V: Units

As described in the [units section](../02-common-principles.md#units),
As described in the [Units](../02-common-principles.md#units),
the specification of units SHOULD follow the
[International System of Units](https://en.wikipedia.org/wiki/International_System_of_Units)
(SI, abbreviated from the French Système international (d'unités)).
Expand All @@ -18,10 +18,10 @@ these are still included for backwards compatibility:
1. [`U+03A9` (Ω)](https://codepoints.net/U+03A9) or [`U+2126` (Ω)](https://codepoints.net/U+2126)
1. [`U+00B0` (°)](https://codepoints.net/U+00B0)

Note that for the first two Unicode symbols in the list above, two characters
are permissible for each, but the first character mentioned respectively is
preferred as per Unicode rules (see the section on "Duplicated Characters"
on page 11 in the [unicode report](https://www.unicode.org/reports/tr25/)).
Note that for the first two entries in this list, two characters are permissible
for each, but the first character in each entry is preferred, per Unicode rules
(see the section on "Duplicated Characters" on page 11 in the
[unicode report](https://www.unicode.org/reports/tr25/)).

It is RECOMMENDED that units be CMIXF-12 compliant or among these five Unicode
characters.
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