From 85d459b3ebdf4382ead9f3bf2beedad3de408ca3 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Tue, 7 Nov 2023 15:29:59 +0100 Subject: [PATCH] =?UTF-8?q?=E2=80=99=20->=20'=20(#1649)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/appendices/coordinate-systems.md | 2 +- src/appendices/meg-file-formats.md | 4 ++-- src/common-principles.md | 2 +- src/derivatives/common-data-types.md | 2 +- src/derivatives/introduction.md | 6 +++--- src/modality-specific-files/magnetoencephalography.md | 4 ++-- src/modality-specific-files/microscopy.md | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index 28b50ab9bb..c5b44207bc 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -221,7 +221,7 @@ However, their use is [DEPRECATED][deprecated]. | **Coordinate System** | **Description** | **RECOMMENDED alternative identifier** | | ----------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------- | -| fsaverage\[3\|4\|5\|6\|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template | fsaverage\[Sym\] | +| fsaverage\[3\|4\|5\|6\|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template | fsaverage\[Sym\] | | UNCInfant\[0\|1\|2\]V\[21\|22\|23\] | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | UNCInfant | ### Nonstandard coordinate system identifiers diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md index 6b3730a543..81b640b517 100644 --- a/src/appendices/meg-file-formats.md +++ b/src/appendices/meg-file-formats.md @@ -57,7 +57,7 @@ A guide for using macros can be found at } ) }} -To learn more about CTF’s data organization +To learn more about CTF's data organization on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/ctf/) ## Neuromag/Elekta/MEGIN @@ -408,7 +408,7 @@ header that contains detailed information about the data acquisition system, followed by binary data. The associated binary header file contains part of the information from the ASCII header, specifically the one needed to process data, plus other information on offline preprocessing performed after data acquisition -(for example, sensor position relative to subject’s head, head markers, stimulus +(for example, sensor position relative to subject's head, head markers, stimulus information). Example: diff --git a/src/common-principles.md b/src/common-principles.md index 2dc9905d9a..83d0b0e2c4 100644 --- a/src/common-principles.md +++ b/src/common-principles.md @@ -393,7 +393,7 @@ include a `dataset_description.json` file at the root level (see [Dataset description][dataset-description]). Consequently, files should be organized to comply with BIDS to the full extent possible (that is, unless explicitly contradicted for derivatives). -Any subject-specific derivatives should be housed within each subject’s directory; +Any subject-specific derivatives should be housed within each subject's directory; if session-specific derivatives are generated, they should be deposited under a session subdirectory within the corresponding subject directory; and so on. diff --git a/src/derivatives/common-data-types.md b/src/derivatives/common-data-types.md index cf149c42b6..486e733790 100644 --- a/src/derivatives/common-data-types.md +++ b/src/derivatives/common-data-types.md @@ -249,7 +249,7 @@ A guide for using macros can be found at } ) }} -All REQUIRED metadata fields coming from a derivative file’s source file(s) MUST +All REQUIRED metadata fields coming from a derivative file's source file(s) MUST be propagated to the JSON description of the derivative unless the processing makes them invalid (for example, if a source 4D image is averaged to create a single static volume, a `RepetitionTime` property would no longer be relevant). diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md index 9cad29a14a..669719cdc1 100644 --- a/src/derivatives/introduction.md +++ b/src/derivatives/introduction.md @@ -39,13 +39,13 @@ in [Derived dataset and pipeline description][derived-dataset-description]. pertinent fields is very valuable and thus encouraged. Moreover, for some types of files, there may be one or more required metadata fields, in which case at least one metadata file containing that field must be located - somewhere within the file’s hierarchy (per the + somewhere within the file's hierarchy (per the [Inheritance Principle](../common-principles.md#the-inheritance-principle)). - When chaining derivative pipelines, any JSON fields that were specified as mandatory in the input files SHOULD be propagated forward in the output - file’s JSON provided they remain valid. Non-required JSON fields MAY be - propagated, and are highly useful, but it is the pipeline’s responsibility + file's JSON provided they remain valid. Non-required JSON fields MAY be + propagated, and are highly useful, but it is the pipeline's responsibility to ensure that the values are still relevant and appropriate to the type of output data. diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md index 369b86fddf..53b0a2edfe 100644 --- a/src/modality-specific-files/magnetoencephalography.md +++ b/src/modality-specific-files/magnetoencephalography.md @@ -442,7 +442,7 @@ and a guide for using macros can be found at {{ MACROS___make_filename_template("raw", datatypes=["meg"], suffixes=["photo"]) }} Photos of the anatomical landmarks and/or head localization coils on the -subject’s head are RECOMMENDED. If the coils are not placed at the location of +subject's head are RECOMMENDED. If the coils are not placed at the location of actual anatomical landmarks, these latter may be marked with a piece of felt-tip taped to the skin. Please note that the photos may need to be cropped or blurred to conceal identifying features prior to sharing, depending on the terms of the @@ -476,7 +476,7 @@ The 3-D locations of points that describe the head shape and/or EEG electrode locations can be digitized and stored in separate files. The [`acq-