FIX: update usage documentation

Author: mnoergaard

docs/outputs.rst

@@ -57,14 +57,14 @@ The log directory contains `citation boilerplate`_ text.
 ``dataset_description.json`` is a metadata file in which PETPrep
 records metadata recommended by the BIDS standard.
 
-This layout, now the default, may be explicitly specified with the
+This default layout, may be explicitly specified with the
 ``--output-layout bids`` command-line option.
-For compatibility with versions of PETPrep prior to 21.0, the
+For compatibility with versions of fMRIPrep prior to 21.0, the
 `legacy layout`_ is available via ``--output-layout legacy``.
 
 Processing level
 ----------------
-As of version 23.2.0, PETPrep supports three levels of derivatives:
+As of version 0.0.1, PETPrep supports three levels of derivatives:
 
 * ``--level minimal``: This processing mode aims to produce the smallest
   working directory and output dataset possible, while enabling all further
@@ -73,13 +73,9 @@ As of version 23.2.0, PETPrep supports three levels of derivatives:
   preprocessing can be assessed. Because no resampling is done, confounds
   and carpetplots will be missing from the reports.
 * ``--level resampling``: This processing mode aims to produce additional
-  derivatives that enable third-party resampling, resampling PET series
+  derivatives that enable third-party resampling, resampling PET data
   in the working directory as needed, but these are not saved to the output
   directory.
-  The ``--me-output-echos`` flag will be enabled at this level, in which
-  case the individual echos will be saved to the working directory after
-  slice-timing correction, head-motion correction, and susceptibility
-  distortion correction.
 * ``--level full``: This processing mode aims to produce all derivatives
   that have previously been a part of the PETPrep output dataset.
   This is the default processing level.
@@ -197,7 +193,7 @@ and lookup tables are provided. ::
       desc-aparcaseg_dseg.tsv
 
 Copies of the ``fsaverage`` subjects distributed with the running version of
-FreeSurfer are copied into this subjects directory, if any functional data are
+FreeSurfer are copied into this subjects directory, if any PET data are
 sampled to those subject spaces.
 
 Note that the use of ``sourcedata/`` recognizes FreeSurfer derivatives as an input to
@@ -206,16 +202,14 @@ This is strictly true when pre-computed FreeSurfer derivatives are provided eith
 the ``sourcedata/`` directory or passed via the ``--fs-subjects-dir`` flag;
 if PETPrep runs FreeSurfer, then there is a mutual dependency.
 
-Functional derivatives
+PET derivatives
 ~~~~~~~~~~~~~~~~~~~~~~
-Functional derivatives are stored in the ``func/`` subfolder.
-All derivatives contain ``task-<task_label>`` (mandatory) and ``run-<run_index>`` (optional), and
-these will be indicated with ``[specifiers]``::
+PET derivatives are stored in the ``pet/`` subfolder.
 
   sub-<subject_label>/
     func/
-      sub-<subject_label>_[specifiers]_space-<space_label>_desc-brain_mask.nii.gz
-      sub-<subject_label>_[specifiers]_space-<space_label>_desc-preproc_pet.nii.gz
+      sub-<subject_label>_space-<space_label>_desc-brain_mask.nii.gz
+      sub-<subject_label>_space-<space_label>_desc-preproc_pet.nii.gz
 
 .. note::
 
@@ -251,27 +245,6 @@ image and affine transform::
 
    Coregistration outputs are part of the *minimal* processing level.
 
-**Fieldmap registration**.
-
-If a fieldmap is used for the correction of a PET series, then a registration
-is calculated between the PET series and the fieldmap. If, for example, the fieldmap
-is identified with ``"B0Identifier": "TOPUP"``, the generated transform will be named::
-
-  sub-<subject_label>/
-    func/
-      sub-<subject_label>_[specifiers]_from-petref_to-TOPUP_mode-image_xfm.txt
-
-If the association is discovered through the ``IntendedFor`` field of the
-fieldmap metadata, then the transform will be given an auto-generated name::
-
-  sub-<subject_label>/
-    func/
-      sub-<subject_label>_[specifiers]_from-petref_to-auto000XX_mode-image_xfm.txt
-
-.. note::
-
-   Fieldmap registration outputs are part of the *minimal* processing level.
-
 **Regularly gridded outputs (images)**.
 Volumetric output spaces labels (``<space_label>`` above, and in the following) include
 ``T1w`` and ``MNI152NLin2009cAsym`` (default).
@@ -285,7 +258,7 @@ mid-thickness surface mesh::
     func/
       sub-<subject_label>_[specifiers]_space-T1w_desc-aparcaseg_dseg.nii.gz
       sub-<subject_label>_[specifiers]_space-T1w_desc-aseg_dseg.nii.gz
-      sub-<subject_label>_[specifiers]_hemi-[LR]_space-<space_label>_bold.func.gii
+      sub-<subject_label>_[specifiers]_hemi-[LR]_space-<space_label>_pet.func.gii
 
 Surface output spaces include ``fsnative`` (full density subject-specific mesh),
 ``fsaverage`` and the down-sampled meshes ``fsaverage6`` (41k vertices) and
@@ -438,9 +411,6 @@ frames with sudden and large motion or intensity spikes.
 - ``dvars`` - the derivative of RMS variance over voxels (or :abbr:`DVARS (derivative of
   RMS variance over voxels)`) [Power2012]_;
 - ``std_dvars`` - standardized :abbr:`DVARS (derivative of RMS variance over voxels)`;
-- ``non_steady_state_outlier_XX`` - columns indicate non-steady state volumes with a single
-  ``1`` value and ``0`` elsewhere (*i.e.*, there is one ``non_steady_state_outlier_XX`` column per
-  outlier/volume).
 
 Detected outliers can be further removed from time series using methods such as:
 volume *censoring* - entirely discarding problematic time points [Power2012]_,
@@ -648,14 +618,14 @@ See implementation on :mod:`~petprep.workflows.pet.confounds.init_pet_confs_wf`.
 Legacy layout
 -------------
 
-Prior to PETPrep 21.0, the following organizational structure was used::
+Prior to tools such as fMRIPrep 21.0, the following organizational structure was used::
 
     <output_dir>/
-      petprep/
+      fmriprep/
       freesurfer/
 
 Although this has the advantage of keeping all outputs together,
-it ensured that the output of PETPrep could not itself be a BIDS derivative dataset,
+it ensured that the output of fMRIPrep could not itself be a BIDS derivative dataset,
 only contain one.
 
 To restore this behavior, use the ``--output-layout legacy`` command-line option.