[skip ds210][skip ds054] update the documentation

Author: jdkent

docs/workflows.rst

@@ -588,6 +588,10 @@ be generated, so non-aggressive denoising can be manually performed in the T1w s
         -d sub-<subject_label>_task-<task_id>_bold_MELODICmix.tsv \
         -o sub-<subject_label>_task-<task_id>_bold_space-<space>_AromaNonAggressiveDenoised.nii.gz
 
+*Note*: The non-steady state volumes are removed for the determination of components in melodic.
+Therefore ``*MELODICmix.tsv`` may have zero padded rows to account for the volumes not used in 
+melodic's estimation of components.
+
 A visualization of the AROMA component classification is also included in the HTML reports.
 
 .. figure:: _static/aroma.svg

fmriprep/workflows/bold/confounds.py

@@ -397,6 +397,7 @@ def init_ica_aroma_wf(template, metadata, mem_gb, omp_nthreads,
 
     The following steps are performed:
 
+    #. Remove non-steady state volumes from the bold series.
     #. Smooth data using FSL `susan`, with a kernel width FWHM=6.0mm.
     #. Run FSL `melodic` outside of ICA-AROMA to generate the report
     #. Run ICA-AROMA
@@ -426,40 +427,53 @@ def init_ica_aroma_wf(template, metadata, mem_gb, omp_nthreads,
 
     **Parameters**
 
+        aroma_melodic_dim: int or None
+            Set the dimensionality of the Melodic ICA decomposition
+            If None, MELODIC automatically estimates dimensionality.
+        ignore_aroma_err : bool
+            Do not fail on ICA-AROMA errors
+        mem_gb : float
+            Size of BOLD file in GB
+        metadata : dict
+            BIDS metadata for BOLD file
+        name : str
+            Name of workflow (default: ``bold_mni_trans_wf``)
+        omp_nthreads : int
+            Maximum number of threads an individual process may use
         template : str
             Spatial normalization template used as target when that
             registration step was previously calculated with
             :py:func:`~fmriprep.workflows.bold.registration.init_bold_reg_wf`.
             The template must be one of the MNI templates (fMRIPrep uses
             ``MNI152NLin2009cAsym`` by default).
-        metadata : dict
-            BIDS metadata for BOLD file
-        mem_gb : float
-            Size of BOLD file in GB
-        omp_nthreads : int
-            Maximum number of threads an individual process may use
-        name : str
-            Name of workflow (default: ``bold_mni_trans_wf``)
         susan_fwhm : float
             Kernel width (FWHM in mm) for the smoothing step with
             FSL ``susan`` (default: 6.0mm)
         use_fieldwarp : bool
             Include SDC warp in single-shot transform from BOLD to MNI
-        ignore_aroma_err : bool
-            Do not fail on ICA-AROMA errors
-        aroma_melodic_dim: int or None
-            Set the dimensionality of the Melodic ICA decomposition
-            If None, MELODIC automatically estimates dimensionality.
 
 
     **Inputs**
-
-        bold_mni
-            BOLD series, resampled to template space
+        bold_mask
+            BOLD series mask in template space
+        bold_split
+            Individual 3D BOLD volumes, not motion corrected
+        fieldwarp
+            a :abbr:`DFM (displacements field map)` in ITK format
+        hmc_xforms
+            List of affine transforms aligning each volume to ``ref_image`` in ITK format
+        itk_bold_to_t1
+            Affine transform from ``ref_bold_brain`` to T1 space (ITK format)
         movpar_file
             SPM-formatted motion parameters file
-        bold_mask_mni
-            BOLD series mask in template space
+        n_volumes_to_discard
+            number of non steady state volumes
+        name_source
+            BOLD series NIfTI file
+            Used to recover original information lost during processing
+        t1_2_mni_forward_transform
+            ANTs-compatible affine-and-warp transform file
+
 
     **Outputs**
 
@@ -472,15 +486,15 @@ def init_ica_aroma_wf(template, metadata, mem_gb, omp_nthreads,
         nonaggr_denoised_file
             BOLD series with non-aggressive ICA-AROMA denoising applied
 
-    .. _ICA-AROMA: https://github.com/rhr-pruim/ICA-AROMA
+    .. _ICA-AROMA: https://github.com/maartenmennes/ICA-AROMA
 
     """
     workflow = Workflow(name=name)
     workflow.__postdesc__ = """\
 Automatic removal of motion artifacts using independent component analysis
 [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space*
-time-series after a spatial smoothing with an isotropic, Gaussian kernel
-of 6mm FWHM (full-width half-maximum).
+time-series after removal of non-steady state volumes and spatial smoothing
+with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum).
 Corresponding "non-aggresively" denoised runs were produced after such
 smoothing.
 Additionally, the "aggressive" noise-regressors were collected and placed