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+# Functional derivatives
+
+## Functional derivatives maps
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func/
+            <source_keywords>[_space-<space>][_desc-<label>]_<suffix>.nii[.gz]
+            <source_keywords>[_space-<space>][_desc-<label>]_<suffix>.json
+```
+
+for example:
+
+```Text
+pipeline1/
+    sub-001/
+        func/
+            sub-001_task-rest_run-1_space-MNI305_mean.nii.gz
+            sub-001_task-rest_run-1_space-MNI305_mean.json
+```
+
+The following table lists allowed suffixes and their corresponding measures:
+
+| `<suffix>`       | Measure                                                          |
+| ---------------- | ---------------------------------------------------------------- |
+| `mean`           | Mean across the temporal/4th dimension of the data               |
+| `std`            | Standard deviation across the temporal/4th dimension of the data |
+| `tsnr`           | Temporal SNR (i.e. mean / std)                                   |
+| `sfs`            | Signal fluctuation sensitivity                                   |
+| `alff`           | Amplitude low frequency fluctuations                             |
+| `falff`          | Fractional amplitude of low frequency fluctuations               |
+| `reho`           | Regional homogeneity (voxelwise only)                            |
+| `dcb`, `dcw`     | Voxelwise degree centrality binary and weighted                  |
+| `ecb`, `ecw`     | Voxelwise eigenvector centrality binary and weighted             |
+| `lfcdb`, `lfcdw` | Local functional connectivity density                            |
+| `vmhc`           | Voxel mirrored homotopic connectivity                            |
+
+The following metadata JSON fields are valid for derivative maps:
+
+| Key name       | Description                                                               | Required for suffix        |
+| -------------- | ------------------------------------------------------------------------- | -------------------------- |
+| BandpassFilter | String describing all relevant parameters of the applied bandpass filter. | `alff`, `falff`            |
+| Neighborhood   | String describing neighborhood for regional measures.                     | `reho`                     |
+| Threshold      | String describing threshold used for determining graph edges.             | `dcb`, `dcw`, `ecb`, `ecw` |
+| Method         | String describing method used to calculate measure.                       | `dcb`, `dcw`, `ecb`, `ecw` |
+
+## Time series
+
+A time series is a chronologically ordered series of numeric values.
+Time series will generally be stored as tables, with a row of column headers
+indicating the name of the series.
+In the case where every voxel has a time series, then the data should be stored
+in a 4D NIfTI file.
+
+All time series files MUST be accompanied by a data dictionary in JSON format,
+consistent with the format described in
+[Common principles](../02-common-principles.md#tabular-files), which describes
+metadata for each column name.
+In the case of NIfTI time series files, the notion of column name does not
+apply, so column-level metadata may be applied to the entire file.
+In addition, the following fields apply to the entire file in all cases:
+
+| Field name        | Definition                                                                                                                                                   |
+| :---------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all columns in the file. Special value `"TR"` indicates one sample per volume of a corresponding BOLD series.        |
+| StartTime         | OPTIONAL. Start time in seconds in relation to the start of acquisition of the first volume in the corresponding imaging file (negative values are allowed). |
+
+Note that there are several differences with these fields in
+[Physiological and other continuous recordings](../04-modality-specific-files/06-physiological-and-other-continuous-recordings.md).
+The `"TR"` sampling frequency serves to indicate that no resampling is needed
+to use the series as a regressor for BOLD data, including BOLD series with
+non-uniform sampling, such as clustered sparse acquisition.
+`StartTime` is assumed to be 0 and therefore not mandatory.
+Additionally, because time series TSV files have column headers, the `Columns`
+field is omitted.
+
+### General time series
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func/
+	        <source_keywords>[_desc-<label>]_timeseries.tsv
+	        <source_keywords>[_desc-<label>]_timeseries.json
+```
+
+for example:
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_desc-confounds_timeseries.tsv
+        sub-001_task-rest_run-1_desc-confounds_timeseries.json
+```
+
+Any time series with common timing information may be stored in a `timeseries`
+file.
+If a time series is specified in another sub-section, then any additional
+required metadata MUST be stored in the JSON description of the column.
+
+#### Column names
+
+Column names are unique alphanumeric values that are defined in a relevant JSON
+sidecar file. For a series of related columns, it is RECOMMENDED to use
+zero-based indexing as a suffix. For example, the first six aCompCor components
+may be named `a_comp_cor_00` ... `a_comp_cor_05`. Custom column names must not
+conflict with reserved names specified in this document.
+
+Reserved names are specified in the remaining subsections.
+
+#### Time series transformations
+
+Any column may have the following suffixes appended to indicate transformations
+applied to the original time series data:
+
+| Transformation | Description                                                                 |
+| -------------- | --------------------------------------------------------------------------- |
+| `_shift_back`  | The time series has been lagged by one TR. `x_shift_back[i] = x[i-1]`       |
+| `_dt`          | The discrete first derivative of the time series. `x_dt[i] = x[i+1] - x[i]` |
+| `_sq`          | The square of the time series                                               |
+| `_var_norm`    | The time series has been variance normalized                                |
+| `_centered`    | The time series has had its mean subtracted                                 |
+
+For example, `rot_z_shift_back_sq` means the square of the lagged version of the
+Z rotation (see [Motion-related time series](#motion-related-time-series)).
+
+### ROI-based time series extraction
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func/
+            <source_keywords>[_atlas-<atlas_label>][_desc-<label>]_timeseries.<tsv|nii[.gz]>
+            <source_keywords>[_atlas-<atlas_label>][_desc-<label>]_timeseries.json
+```
+
+for example:
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_atlas-AAL_timeseries.tsv
+        sub-001_task-rest_run-1_atlas-AAL_timeseries.json
+        sub-001_task-rest_run-1_desc-anaticor_timeseries.nii.gz
+        sub-001_task-rest_run-1_desc-anaticor_timeseries.json
+```
+
+ROI-based time series will generally be stored as tables, with a row of column
+headers indicating the name of the time series.
+In the case where every voxel has a time series (i.e., voxel-wise regressors,
+as in ANATICOR), then the time series should be saved as a NIfTI file.
+
+#### Column metadata special fields
+
+Atlas (optional) - A label indicating an atlas that defines a region or set of
+regions in the volume. An atlas may be three- or four-dimensional, which affects
+the interpretation of the roi index.
+
+ROI (optional) - For 3D atlases, the ROI label should be numeric, corresponding
+to the value of the voxels in the ROI. For 4D atlases, the ROI label should be
+numeric, corresponding to the volume index containing the ROI mask. The
+following special labels correspond to common ROIs that may be defined by many
+atlases or segmentation algorithms:
+
+| ROI Value      | Description                                                                            |
+| -------------- | -------------------------------------------------------------------------------------- |
+| WhiteMatter    | Signal derived from white matter ROI.                                                  |
+| CSF            | Signal derived from cerebro-spinal fluid ROI.                                          |
+| Background     | Signal derived from background (out of brain) ROI.                                     |
+| GrayMatter     | Signal derived from gray matter ROI.                                                   |
+| Ventricles     | Signal derived from ventricles ROI.                                                    |
+| CircleOfWillis | Signal derived from circle of Willis ROI.                                              |
+| GlobalSignal   | Vector of mean values within the brain mask. Can be used for Global Signal Regression. |
+
+#### Column names
+
+Column names are unique alphanumeric values that are defined in a relevant JSON
+sidecar file. A naming convention might be to concatenate the atlas, ROI index,
+summarization method (defined below) and transformations (see [Time series
+transformations](#time-series-transformations)) using snake case. For example,
+`harvard_oxford_cortical_4_PC` could indicate ROI 4 of the Harvard-Oxford
+cortical atlas, summarized by taking the first principal component.
+
+#### Summarization methods
+
+To indicate the summarization method applied to construct a single time series
+for an ROI, the following column suffixes are defined:
+
+| Column suffix | Description of the transformation                                                                                                                       |
+| ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `_mean`       | The mean of voxel time series                                                                                                                           |
+| `_median`     | The median of voxel time series                                                                                                                         |
+| `_pc[_<x>]`   | The ith eigenvariate from principal component analysis, where `x` is 0 indexed. If `x` is not specified, the first component is implied (i.e., `pc_0`). |
+| `_spat_reg`   | Spatial regression                                                                                                                                      |
+
+Example:
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_timeseries.tsv
+```
+
+```Text
+white_matter_mean global_signal_mean ventricles_mean
+12                98                 11
+11                34                 53
+54                34                 34
+```
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_timeseries.json
+```
+
+```JSON
+{
+    "SamplingFrequency": "TR",
+    "white_matter_mean": {
+        "ROI": "WhiteMatter"
+    },
+    "global_signal_mean": {
+        "ROI": "GlobalSignal"
+    },
+    "ventricles_mean": {
+        "ROI": "Ventricles"
+    }
+}
+```
+
+### Motion-related time series
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+    func/
+        <source_keywords>[_desc-<label>]_motion.tsv
+        <source_keywords>[_desc-<label>]_motion.json
+```
+
+#### Column names
+
+The six basic motion parameters derived from motion correction have the
+following names and units:
+
+| Column name                     | Units   | Description            |
+| ------------------------------- | ------- | ---------------------- |
+| `trans_x`, `trans_y`, `trans_z` | mm      | Translation parameters |
+| `rot_x`, `rot_y`, `rot_z`       | radians | Rotation parameters    |
+
+Transformations (see [Time series
+transformations](#time-series-transformations)) of motion parameters may be
+included in the same file.
+For example, `rot_z_shift_back_sq` means square of the lagged version of Z
+rotation.
+
+The following columns indicate summarized motion, as defined in the
+corresponding references:
+
+| Column name              | Units | Description                                                         |
+| ------------------------ | ----- | ------------------------------------------------------------------- |
+| `framewise_displacement` | mm    | Framewise displacement (Power, et al., 2012)                        |
+| `rmsd`                   | mm    | Root mean square deviation (Jenkinson, 1999)                        |
+| `rms`                    | mm    | Root mean square of translation parameters (Van Dijk, et al., 2012) |
+
+### Temporal outlier masks
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func/
+	        <source_keywords>[_desc-<label>]_outliers.tsv
+            <source_keywords>[_desc-<label>]_outliers.json
+```
+
+Outlier masks are columns of zeros (0), with ones (1) indicating volumes that
+have been identified as outliers by some method.
+
+#### Column names
+
+Column names for outliers correspond to the type of outlier or method for
+identifying the outlier. Column names should take the form `method[XX]`, where
+`XX` is an optional index.
+
+For example, if a BOLD series included two initial dummy scans,
+`non_steady_state` may be a column with a 1 for the first two volumes, or
+`non_steady_state_00` and `non_steady_state_01` may be columns with a 1 in the
+first and second position, respectively.
+
+The following methods are defined as reserved words:
+
+| Column name            | Description                                              |
+| ---------------------- | -------------------------------------------------------- |
+| `non_steady_state_<x>` | Initial non-steady-state volumes. One column per volume. |
+
+### Other time series
+
+Time series that are not otherwise specified MUST be placed in a
+`_timeseries.tsv` file (see [General time series](#general-time-series)).
+
+#### Column names
+
+The following time series are defined as reserved words:
+
+| Column name    | Description                                           |
+| -------------- | ----------------------------------------------------- |
+| `dvars`        | Change in variance (Brett, 2006, Power, et al., 2012) |
+| `std_dvars`    | Standardized DVARS (Nichols, 2013)                    |
+| `cosine_<X>`   | Discrete cosine basis vectors                         |
+| `legendre_<X>` | Legendre polynomial basis vectors                     |
+
+### Spatiotemporal decompositions
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<participant_label>/
+        func/
+            <source_keywords>[_desc-<label>]_<mixing|components>.tsv
+            <source_keywords>[_desc-<label>]_<mixing|components>.nii.gz
+            <source_keywords>[_desc-<label>]_decomposition.json
+```
+
+for example:
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_desc-MELODIC_components.nii.gz
+        sub-001_task-rest_run-1_desc-MELODIC_mixing.tsv
+        sub-001_task-rest_run-1_desc-MELODIC_decomposition.json
+```
+
+```Text
+sub-001/
+    func/
+        sub-001_task-rest_run-1_desc-tICA_mixing.nii.gz
+        sub-001_task-rest_run-1_desc-tICA_components.tsv
+        sub-001_task-rest_run-1_desc-tICA_decomposition.json
+```
+
+Spatiotemporal decompositions produce either spatial or temporal components,
+along with conjugate mixing matrices that can be represented as time series and
+spatial maps, respectively. The combination of suffix and extension indicates
+which class of algorithm produced the outputs.
+
+Mixing matrices may be omitted for algorithms that are temporal decompositions
+with no spatial component, such as CompCor variants.
+
+Spatiotemporal decomposition files MUST be accompanied by a data dictionary in
+JSON format, consistent with Raw-BIDS section 4.2, which describes metadata for
+each column name. In addition to column names, the following MANDATORY field is
+added:
+
+| Key name | Description                                           |
+| -------- | ----------------------------------------------------- |
+| Method   | REQUIRED. Algorithm name and (if applicable) version. |
+
+#### Column names
+
+Column names in spatiotemporal decompositions take the form of
+`<decomposition>_<index>`, where `<decomposition>` is the name of the
+decomposition algorithm, and `<index>` is a numeric identifier. Indices SHOULD
+start at 0. If there is a natural ordering, indices should reflect that
+ordering. For example, the aCompCor component which explains the most variance
+should be named `a_comp_cor_00`.
+
+The following reserved words indicate common algorithms:
+
+| Column name              | Description                                                                                                                                                                                                |
+| ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `[a|t|w|c]_comp_cor_<x>` | CompCor (Behzadi, et al., 2007) calculated with voxels chosen based on: `a`: anatomically derived ROIs (white matter and CSF), `t`: temporal variance, `w`: white matter voxels only, `c`: CSF voxels only |
+| `melodic_<x>`            | Columns from the mixing matrix in FSL MELODIC                                                                                                                                                              |