Merge branch 'master' into meg/name

README.md

@@ -27,6 +27,7 @@ BIDS currently supports the following data modalities with more to come in the f
 - physiological
 - PET
 - microscopy
+- fNIRS
 
 # Formatting your data with BIDS
 

mkdocs.yml

@@ -65,6 +65,7 @@ nav:
         - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md
         - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md
         - Microscopy: 04-modality-specific-files/10-microscopy.md
+        - Functional Near-Infrared Spectroscopy: 04-modality-specific-files/11-functional-near-infrared-spectroscopy.md
       - Derivatives:
         - BIDS Derivatives: 05-derivatives/01-introduction.md
         - Common data types and metadata: 05-derivatives/02-common-data-types.md

src/01-introduction.md

@@ -156,6 +156,10 @@ For example:
     **qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data.**
     Scientific Data 9, 517 (2022). [doi:10.1038/s41597-022-01571-4](https://doi.org/10.1038/s41597-022-01571-4)
 
+#### NIRS
+
+-   (publication forthcoming)
+
 ### Research Resource Identifier (RRID)
 
 BIDS has also a

src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md

@@ -172,7 +172,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["anat"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["anat"]) }}
 
 Currently supported non-parametric structural MR images include:
 
@@ -364,7 +364,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["func"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["func"]) }}
 
 Functional imaging consists of techniques that support rapid temporal repetition.
 This includes, but is not limited to, task based fMRI, as well as resting state fMRI, which is treated like any other task.
@@ -572,7 +572,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["dwi"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["dwi"]) }}
 
 The [`run-<index>`](../appendices/entities.md#run) entity is RECOMMENDED
 to encode the splits of multipart DWI scans
@@ -782,7 +782,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["perf"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["perf"]) }}
 
 The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order,
 accompanied by two ancillary files: `*_asl.json` and `*_aslcontext.tsv`.
@@ -1014,7 +1014,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["phasediff", "magnitude1", "magnitude2"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["phasediff", "magnitude1", "magnitude2"]) }}
 
 where
 the REQUIRED `_phasediff` image corresponds to the phase-drift map between echo times,
@@ -1060,7 +1060,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["phase1", "phase2", "magnitude1", "magnitude2"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["phase1", "phase2", "magnitude1", "magnitude2"]) }}
 
 Required fields:
 
@@ -1096,7 +1096,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["fieldmap", "magnitude"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["fieldmap", "magnitude"]) }}
 
 Required fields:
 
@@ -1145,7 +1145,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["fmap"], suffixes=["epi"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["epi"]) }}
 
 The [`dir-<label>`](../appendices/entities.md#dir) entity is REQUIRED
 for these files.

src/04-modality-specific-files/02-magnetoencephalography.md

@@ -24,6 +24,7 @@ and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filename_template(
+   "raw",
    datatypes=["meg"],
    suffixes=["meg", "markers", "events", "physio", "stim"])
 }}
@@ -207,7 +208,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["channels"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["meg"], suffixes=["channels"]) }}
 
 This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
 For example for general curation, response to queries, or for batch analysis.
@@ -291,7 +292,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["coordsystem"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["meg"], suffixes=["coordsystem"]) }}
 
 OPTIONAL. A JSON document specifying the coordinate system(s) used for the MEG,
 EEG, head localization coils, and anatomical landmarks.
@@ -404,7 +405,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["photo"]) }}
+{{ 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
@@ -431,7 +432,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["meg"], suffixes=["headshape"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["meg"], suffixes=["headshape"]) }}
 
 This file is RECOMMENDED.
 

src/04-modality-specific-files/03-electroencephalography.md

@@ -20,6 +20,7 @@ and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filename_template(
+   "raw",
    datatypes=["eeg"],
    suffixes=["eeg", "events", "physio", "stim"])
 }}
@@ -187,7 +188,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["channels"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["eeg"], suffixes=["channels"]) }}
 
 This file is RECOMMENDED as it provides easily searchable information across BIDS datasets.
 For example for general curation, response to queries, or for batch analysis.
@@ -262,7 +263,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["electrodes"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["eeg"], suffixes=["electrodes"]) }}
 
 File that gives the location of EEG electrodes. Note that coordinates are
 expected in cartesian coordinates according to the `EEGCoordinateSystem` and
@@ -309,7 +310,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["coordsystem"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["eeg"], suffixes=["coordsystem"]) }}
 
 A `*_coordsystem.json` file is used to specify the fiducials, the location of
 anatomical landmarks, and the coordinate system and units in which the position
@@ -427,7 +428,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["eeg"], suffixes=["photo"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["eeg"], suffixes=["photo"]) }}
 
 Photos of the anatomical landmarks and/or fiducials are OPTIONAL.
 Please note that the photos may need to be cropped or blurred to conceal

src/04-modality-specific-files/04-intracranial-electroencephalography.md

@@ -20,6 +20,7 @@ and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filename_template(
+   "raw",
    datatypes=["ieeg"],
    suffixes=["ieeg", "events", "physio", "stim"])
 }}
@@ -207,7 +208,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["channels"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["ieeg"], suffixes=["channels"]) }}
 
 A channel represents one time series recorded with the recording system
 (for example, there can be a bipolar channel, recorded from two electrodes or contact points on the tissue).
@@ -280,7 +281,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["electrodes"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["ieeg"], suffixes=["electrodes"]) }}
 
 File that gives the location, size and other properties of iEEG electrodes. Note
 that coordinates are expected in cartesian coordinates according to the
@@ -354,7 +355,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["coordsystem"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["ieeg"], suffixes=["coordsystem"]) }}
 
 This `_coordsystem.json` file contains the coordinate system in which electrode
 positions are expressed. The associated MRI, CT, X-Ray, or operative photo can
@@ -434,7 +435,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["ieeg"], suffixes=["photo"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["ieeg"], suffixes=["photo"]) }}
 
 These can include photos of the electrodes on the brain surface, photos of
 anatomical features or landmarks (such as sulcal structure), and fiducials. Photos

src/04-modality-specific-files/07-behavioral-experiments.md

@@ -7,7 +7,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["beh"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["beh"]) }}
 
 In addition to logs from behavioral experiments performed alongside imaging data
 acquisitions, one can also include data from experiments performed with no neural

src/04-modality-specific-files/09-positron-emission-tomography.md

@@ -68,6 +68,7 @@ and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filename_template(
+   "raw",
    datatypes=["pet"],
    suffixes=["pet", "events", "physio", "stim"])
 }}
@@ -300,7 +301,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["pet"], suffixes=["blood"]) }}
+{{ MACROS___make_filename_template("raw", datatypes=["pet"], suffixes=["blood"]) }}
 
 If collected, blood measurements of radioactivity are be stored in
 [Tabular files](../02-common-principles.md#tabular-files) and located in

src/04-modality-specific-files/10-microscopy.md

@@ -25,7 +25,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
+{{ MACROS___make_filename_template("raw", datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
 "PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }}
 
 Microscopy data MUST be stored in the `micr` directory.
@@ -438,7 +438,7 @@ The inputs for this macro can be found in the folder
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_filename_template(datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
+{{ MACROS___make_filename_template("raw", datatypes=["micr"], suffixes=["photo"], n_dupes_to_combine=3) }}
 
 The file `<extension>` for photos MUST be either `.jpg`, `.png` or `.tif`.