Document the nichart mode (#1325)

docs/workflows.rst

@@ -32,7 +32,7 @@ Starting in version 0.8.0, XCP-D includes a required ``--mode`` parameter.
 The ``mode`` parameter automatically defines sets of other parameters,
 based on recommended processing pipelines for different studies.
 
-XCP-D can be run in one of three modes: ``linc``, ``abcd``, or ``hbcd``.
+XCP-D can be run in one of four modes: ``linc``, ``abcd``, ``hbcd``, or ``nichart``.
 Each mode is designed by a different group, and has different requirements.
 
 Users may also run XCP-D in ``none`` mode, in which case almost all of the parameters must be
@@ -66,6 +66,8 @@ which may be overridden by the user:
 -  ``--fd-thresh 0``: Censoring is disabled by default.
 -  ``--input-type fmriprep``: fMRIPrep outputs are expected as input.
 -  ``--linc-qc``: The LINC QC file will be created by default.
+-  ``--min-coverage 0.5``: The default coverage threshold is 0.5.
+-  ``--smoothing 6``: Smoothing is enabled by default.
 
 Optional Parameters
 -------------------
@@ -116,6 +118,8 @@ which may be overridden by the user:
 -  ``--combine-runs``: Runs will be concatenated by default.
 -  ``--warp-surfaces-native2std``: Surfaces will be warped to standard space by default.
 -  ``--linc-qc``: The LINC QC file will be created by default.
+-  ``--min-coverage 0.5``: The default coverage threshold is 0.5.
+-  ``--smoothing 6``: Smoothing is enabled by default.
 
 Required Parameters
 -------------------
@@ -167,6 +171,8 @@ which may be overridden by the user:
 -  ``--combine-runs``: Runs will be concatenated by default.
 -  ``--warp-surfaces-native2std``: Surfaces will be warped to standard space by default.
 -  ``--linc-qc``: The LINC QC file will be created by default.
+-  ``--min-coverage 0.5``: The default coverage threshold is 0.5.
+-  ``--smoothing 6``: Smoothing is enabled by default.
 
 Required Parameters
 -------------------
@@ -189,6 +195,30 @@ Optional Parameters
    as well as the special value "all", which uses all of the low-motion data from the run.
 
 
+nichart Mode
+============
+
+The ``nichart`` mode is used by the `NiChart project <https://neuroimagingchart.com/>`_.
+
+This mode is very similar to ``linc`` mode, with the exception that it processes NIfTI files
+by default and has smoothing disabled.
+
+Defaults
+--------
+
+By default, the ``nichart`` mode will apply the following parameters,
+which may be overridden by the user:
+
+-  ``--file-format nifti``: NIfTI files are used as input.
+-  ``--despike``: Despiking is enabled by default.
+-  ``--fd-thresh 0``: Motion-based censoring is disabled by default.
+-  ``--input-type fmriprep``: fMRIPrep outputs are expected as input.
+-  ``--linc-qc``: The LINC QC file will be created by default.
+-  ``--min-coverage 0.4``: The default coverage threshold is 0.4 instead of the more common 0.5.
+-  ``--output-type censored``: Censored data are the primary output.
+-  ``--smoothing 0``: Smoothing is disabled by default.
+
+
 Major Differences Between Modes
 ===============================
 

xcp_d/cli/parser.py

@@ -982,11 +982,8 @@ def _validate_parameters(opts, build_log, parser):
         if opts.output_type == 'censored':
             error_messages.append(f"'--output-type' cannot be 'censored' for '{opts.mode}' mode.")
         opts.output_type = 'interpolated'
+        opts.process_surfaces = True if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        opts.confounds_config = '36P' if opts.confounds_config == 'auto' else opts.confounds_config
-        opts.process_surfaces = (
-            True if (opts.process_surfaces == 'auto') else opts.process_surfaces
-        )
         # Remove "all" from the list of correlation lengths
         opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'hbcd':
@@ -1010,11 +1007,8 @@ def _validate_parameters(opts, build_log, parser):
         if opts.output_type == 'censored':
             error_messages.append(f"'--output-type' cannot be 'censored' for '{opts.mode}' mode.")
         opts.output_type = 'interpolated'
+        opts.process_surfaces = True if opts.process_surfaces == 'auto' else opts.process_surfaces
         opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        opts.confounds_config = '36P' if opts.confounds_config == 'auto' else opts.confounds_config
-        opts.process_surfaces = (
-            True if (opts.process_surfaces == 'auto') else opts.process_surfaces
-        )
         # Remove "all" from the list of correlation lengths
         opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'linc':
@@ -1035,9 +1029,8 @@ def _validate_parameters(opts, build_log, parser):
                 f"'--output-type' cannot be 'interpolated' for '{opts.mode}' mode."
             )
         opts.output_type = 'censored'
-        opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
-        opts.confounds_config = '36P' if opts.confounds_config == 'auto' else opts.confounds_config
         opts.process_surfaces = False if opts.process_surfaces == 'auto' else opts.process_surfaces
+        opts.smoothing = 6 if opts.smoothing == 'auto' else opts.smoothing
         if opts.dcan_correlation_lengths is not None:
             error_messages.append(f"'--create-matrices' is not supported for '{opts.mode}' mode.")
     elif opts.mode == 'nichart':
@@ -1057,9 +1050,8 @@ def _validate_parameters(opts, build_log, parser):
         opts.min_coverage = 0.4 if opts.min_coverage == 'auto' else opts.min_coverage
         opts.output_correlations = True if 'all' in opts.dcan_correlation_lengths else False
         opts.output_type = 'censored' if opts.output_type == 'auto' else opts.output_type
-        opts.smoothing = 0 if opts.smoothing == 'auto' else opts.smoothing
-        opts.confounds_config = '36P' if opts.confounds_config == 'auto' else opts.confounds_config
         opts.process_surfaces = False if opts.process_surfaces == 'auto' else opts.process_surfaces
+        opts.smoothing = 0 if opts.smoothing == 'auto' else opts.smoothing
         # Remove "all" from the list of correlation lengths
         opts.dcan_correlation_lengths = [c for c in opts.dcan_correlation_lengths if c != 'all']
     elif opts.mode == 'none':