Calculate correlation variance with scrubbing-aware xDF

README.rst

@@ -50,7 +50,7 @@ Thus, with the development of *XCP-D*, data can be automatically preprocessed an
 format, using NiPrep-style containerized code, all the way from the scanner to functional
 connectivity matrices.
 
-*XCP-D* picks up right where `fMRIprep <https://fmriprep.org>`_ ends, directly consuming the outputs
+*XCP-D* picks up right where `fMRIPrep <https://fmriprep.org>`_ ends, directly consuming the outputs
 of fMRIPrep.
 *XCP-D* leverages the BIDS and NiPreps frameworks to automatically generate denoised BOLD images,
 parcellated time series, functional connectivity matrices, and quality assessment reports.

xcp_d/cli/parser.py

@@ -556,6 +556,19 @@ def _build_parser():
             'Must be a value between zero and one, indicating proportion of the parcel.'
         ),
     )
+    g_parcellation.add_argument(
+        '--correlation-outputs',
+        '--correlation_outputs',
+        dest='correlation_outputs',
+        required=False,
+        default=['auto'],
+        nargs='+',
+        choices=['auto', 'r', 'var_r', 'z', 'var_z'],
+        help=(
+            'Outputs to calculate correlations for. '
+            "If 'auto', the outputs will be inferred from the processing mode. "
+        ),
+    )
 
     g_dcan = parser.add_argument_group('abcd/hbcd mode options')
     g_dcan.add_argument(
@@ -1068,6 +1081,9 @@ def _validate_parameters(opts, build_log, parser):
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
         opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
+        if 'auto' in opts.correlation_outputs:
+            opts.correlation_outputs.remove('auto')
+            opts.correlation_outputs = sorted(set(['r'] + opts.correlation_outputs))
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0.3 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'cifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1091,6 +1107,9 @@ def _validate_parameters(opts, build_log, parser):
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
         opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
+        if 'auto' in opts.correlation_outputs:
+            opts.correlation_outputs.remove('auto')
+            opts.correlation_outputs = sorted(set(['r'] + opts.correlation_outputs))
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0.3 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'cifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1113,6 +1132,9 @@ def _validate_parameters(opts, build_log, parser):
         opts.confounds_config = (
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
+        if 'auto' in opts.correlation_outputs:
+            opts.correlation_outputs.remove('auto')
+            opts.correlation_outputs = sorted(set(['r', 'var_r'] + opts.correlation_outputs))
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'cifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1140,6 +1162,9 @@ def _validate_parameters(opts, build_log, parser):
             '36P' if (opts.confounds_config == 'auto') else opts.confounds_config
         )
         opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else 'all'
+        if 'auto' in opts.correlation_outputs:
+            opts.correlation_outputs.remove('auto')
+            opts.correlation_outputs = sorted(set(['r'] + opts.correlation_outputs))
         opts.despike = True if (opts.despike == 'auto') else opts.despike
         opts.fd_thresh = 0 if (opts.fd_thresh == 'auto') else opts.fd_thresh
         opts.file_format = 'nifti' if (opts.file_format == 'auto') else opts.file_format
@@ -1164,6 +1189,10 @@ def _validate_parameters(opts, build_log, parser):
 
         opts.correlation_lengths = opts.correlation_lengths if opts.correlation_lengths else []
 
+        if 'auto' in opts.correlation_outputs:
+            opts.correlation_outputs.remove('auto')
+            opts.correlation_outputs = sorted(set(['r', 'var_r'] + opts.correlation_outputs))
+
         if opts.despike == 'auto':
             error_messages.append("'--despike' (y or n) is required for 'none' mode.")
 

xcp_d/config.py

@@ -625,6 +625,8 @@ class workflow(_Config):
     """Order of the band-pass filter."""
     min_coverage = None
     """Coverage threshold to apply to parcels in each atlas."""
+    correlation_outputs = None
+    """Correlation measures to output."""
     correlation_lengths = None
     """Produce correlation matrices limited to each requested amount of time.
     If this list includes 'all' then correlations from the full (censored) time series will