Merge pull request #1993 from mgxd/doc/fslr

DOC: Clean up surface outputs

Author: oesteban

docs/outputs.rst

@@ -143,15 +143,14 @@ mid-thickness surface mesh::
 
 Surface output spaces include ``fsnative`` (full density subject-specific mesh),
 ``fsaverage`` and the down-sampled meshes ``fsaverage6`` (41k vertices) and
-``fsaverage5`` (10k vertices, default). Additionally, the BOLD can be resampled to
-``fsLR`` surfaces, a hybrid version of the ``fsaverage`` atlas with both hemispheres
-in precise geographic correspondence, with varying mesh densities: 32k (default), 59k, and 164k.
+``fsaverage5`` (10k vertices, default).
 
 **Grayordinates files**.
-CIFTI is a container format that holds both volumetric (regularly sampled in a grid)
-and surface (sampled on a triangular mesh) samples.
-Sub-cortical time series are volumetric (supported spaces: ``MNI152NLin6Asym``), while cortical
-time series are sampled to surface (supported spaces: ``fsLR``).
+`CIFTI <https://www.nitrc.org/forum/attachment.php?attachid=333&group_id=454&forum_id=1955>`_ is
+a container format that holds both volumetric (regularly sampled in a grid) and surface
+(sampled on a triangular mesh) samples.
+Sub-cortical time series are sampled on a regular grid derived from one MNI template, while
+cortical time series are sampled on surfaces projected from the [Glasser2016]_ template.
 If CIFTI outputs are requested (with the ``--cifti-outputs`` argument), the BOLD series are also
 saved as ``dtseries.nii`` CIFTI2 files::
 
@@ -261,7 +260,7 @@ expansion [Satterthwaite2013]_, providing time series corresponding to the first
 *quadratic terms*, resulting in the total 24 head motion parameters
 (six base motion parameters + six temporal derivatives of six motion parameters +
 12 quadratic terms of six motion parameters and their six temporal derivatives).
-Additionally, *fMRIPrep* returns temporal derivatives and quadratic terms for the 
+Additionally, *fMRIPrep* returns temporal derivatives and quadratic terms for the
 three global signals (``csf``, ``white_matter`` and ``global_signal``)
 to enable applying the 36-parameter denoising strategy proposed by [Satterthwaite2013]_.
 
@@ -313,7 +312,7 @@ It is relevant to mention *effective* because initial time points identified as
 states* are removed before generating the cosine regressors.
 
 .. caution::
-    If your analysis includes separate high-pass filtering, do not include 
+    If your analysis includes separate high-pass filtering, do not include
     ``cosine_XX`` regressors in your design matrix.
 
 .. admonition:: See also
@@ -521,6 +520,11 @@ See implementation on :mod:`~fmriprep.workflows.bold.confounds.init_bold_confs_w
      Movement‐Related effects in fMRI time‐series. Magnetic Resonance in Medicine. 1996.
      doi:`10.1002/mrm.191035031 <https://doi.org/10.1002/mrm.1910350312>`_
 
+  .. [Glasser2016] Glasser MF, Coalson TS Robinson EC, Hacker CD, Harwell J, Yacoub E, Ugurbil K,
+     Andersson J, Beckmann CF, Jenkinson M, Smith SM, Van Essen DC.
+     A multi-modal parcellation of human cerebral cortex. Nature. 2016.
+     doi:`10.1038/nature18933 <https://doi.org/10.1038/nature18933>`_
+
   .. [Hallquist2013] Hallquist MN, Hwang K, Luna B. The Nuisance of Nuisance Regression.
      NeuroImage. 2013. doi:`10.1016/j.neuroimage.2013.05.116
      <https://doi.org/10.1016/j.neuroimage.2013.05.116>`_

docs/spaces.rst

@@ -80,8 +80,7 @@ Please mind that the selected resolutions specified must exist within TemplateFl
 
 When specifying surface spaces (e.g., ``fsaverage``), the legacy identifiers from
 FreeSurfer will be supported (e.g., ``fsaverage5``) although the use of the density
-modifier would be preferred (i.e., ``fsaverage:den-10k`` for ``fsaverage5``). When
-selecting ``fsLR`` surface space without a density label, ``fsLR:den-32k`` will be used.
+modifier would be preferred (i.e., ``fsaverage:den-10k`` for ``fsaverage5``).
 
 Custom standard spaces
 """"""""""""""""""""""

fmriprep/workflows/bold/outputs.py

@@ -22,7 +22,6 @@ def init_func_derivatives_wf(
     output_dir,
     spaces,
     use_aroma,
-    fslr_density=None,
     name='func_derivatives_wf',
 ):
     """
@@ -51,8 +50,6 @@ def init_func_derivatives_wf(
         would lead to resampling on a 2mm resolution of the space).
     use_aroma : :obj:`bool`
         Whether ``--use-aroma`` flag was set.
-    fslr_density : :obj:`str`, optional
-        Density of fsLR surface (32k or 59k)
     name : :obj:`str`
         This workflow's identifier (default: ``func_derivatives_wf``).