fix(docs): remove MNI mentions, add cross-references

Author: oesteban

docs/citing.rst

@@ -250,10 +250,6 @@ Presentations
 Other relevant references
 -------------------------
 
-  .. [Fonov2011] Fonov VS, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL and BDCG,
-      Unbiased average age-appropriate atlases for pediatric studies, NeuroImage 54(1), 2011
-      doi:`10.1016/j.neuroimage.2010.07.033 <https://doi.org/10.1016/j.neuroimage.2010.07.033>`_.
-
   .. [Power2017] Power JD, Plitt M, Kundu P, Bandettini PA, Martin A (2017) Temporal interpolation alters
       motion in fMRI scans: Magnitudes and consequences for artifact detection. PLOS ONE 12(9): e0182939.
       doi:`10.1371/journal.pone.0182939 <https://doi.org/10.1371/journal.pone.0182939>`_.

docs/usage.rst

@@ -7,7 +7,7 @@ Usage
    As of FMRIPREP 1.0.12, the software includes a tracking system
    to report usage statistics and errors. Users can opt-out using
    the ``--notrack`` command line argument.
-   
+
 
 Execution and the BIDS format
 =============================
@@ -38,7 +38,7 @@ Command-Line Arguments
    :nodefaultconst:
 
 
-.. _output_spaces:
+.. _output-spaces:
 
 Defining standard and nonstandard spaces where data will be resampled
 =====================================================================
@@ -71,9 +71,9 @@ the original data gridding.
 However, many users will be interested in utilizing a coarse gridding (typically 2mm isotropic)
 of the target template.
 Such a behavior can be achieved applying modifiers to the template identifier, separated by
-a ``:`` character. 
+a ``:`` character.
 For instance, ``--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym`` will generate
-preprocessed BOLD 4D files on two standard spaces (``MNI152NLin6Asym``, 
+preprocessed BOLD 4D files on two standard spaces (``MNI152NLin6Asym``,
 and ``MNI152NLin2009cAsym``) with the template's 2mm isotropic resolution for
 the data on ``MNI152NLin6Asym`` space and the original BOLD resolution
 (say, e.g., 2x2x2.5 [mm]) for the case of ``MNI152NLin2009cAsym``.
@@ -116,7 +116,7 @@ Additionally, ``--output-spaces`` accepts identifiers of spatial references
 that do not generate *standardized* coordinate spaces:
 
   * ``T1w`` or ``anat``: data are resampled into the individual's anatomical
-    reference generated with the T1w and T2w images available within the 
+    reference generated with the T1w and T2w images available within the
     BIDS structure.
   * ``fsnative``: similarly to the ``anat`` space for volumetric references,
     including the ``fsnative`` space will instruct fMRIPrep to sample the
@@ -189,7 +189,7 @@ make your data available within that system first.
 
 For instance, here at the Poldrack Lab we use Stanford's
 :abbr:`HPC (high-performance computing)` system, called Sherlock.
-Sherlock enables `the following data transfer options 
+Sherlock enables `the following data transfer options
 <https://www.sherlock.stanford.edu/docs/user-guide/storage/data-transfer/>`_.
 
 Alternatively, more comprehensive solutions such as `Datalad

docs/workflows.rst

@@ -91,7 +91,7 @@ Brain extraction, brain tissue segmentation and spatial normalization
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Then, the T1w reference is skull-stripped using a Nipype implementation of
-the ``antsBrainExtraction.sh`` tool (ANTs), which is an atlas-based 
+the ``antsBrainExtraction.sh`` tool (ANTs), which is an atlas-based
 brain extraction workflow:
 
 .. workflow::
@@ -120,7 +120,7 @@ Once the brain mask is computed, FSL ``fast`` is utilized for brain tissue segme
 
 Finally, spatial normalization to standard spaces is performed using ANTs' ``antsRegistration``
 in a multiscale, mutual-information based, nonlinear registration scheme.
-See `output_spaces`_ for information about how standard and nonstandard spaces can
+See :ref:`output-spaces` for information about how standard and nonstandard spaces can
 be set to resample the preprocessed data onto the final output spaces.
 
 
@@ -143,9 +143,9 @@ in the same space and resolution as the T1 image, and follow the naming conventi
 (e.g. ``sub-001_T1w_label-lesion_roi.nii.gz``).
 This file should be placed in the ``sub-*/anat`` directory of the BIDS dataset
 to be run through *fMRIPrep*.
-Because lesion masks are not currently part of the BIDS specification, it is also necessary to 
-include a ``.bidsignore`` file in the root of your dataset directory. This will prevent 
-`bids-validator <https://github.com/bids-standard/bids-validator#bidsignore>`_ from complaining that your dataset not BIDS valid, which prevents 
+Because lesion masks are not currently part of the BIDS specification, it is also necessary to
+include a ``.bidsignore`` file in the root of your dataset directory. This will prevent
+`bids-validator <https://github.com/bids-standard/bids-validator#bidsignore>`_ from complaining that your dataset not BIDS valid, which prevents
 *fMRIPrep* from running. Your ``.bidsignore`` file should include the following line::
 
 *lesion_roi.nii.gz
@@ -491,7 +491,7 @@ This sub-workflow concatenates the transforms calculated upstream (see
 fieldmaps are available--, `EPI to T1w registration`_, and an anatomical-to-standard
 transform from `T1w/T2w preprocessing`_) to map the :abbr:`EPI (echo-planar imaging)`
 image to the standard spaces given by the ``--output-spaces`` argument (see
-`output_spaces`_.
+:ref:`output-spaces`.
 It also maps the T1w-based mask to each of those standard spaces.
 
 Transforms are concatenated and applied all at once, with one interpolation (Lanczos)
@@ -560,7 +560,7 @@ ICA-AROMA
 
 ICA-AROMA denoising is performed in ``MNI152NLin6Asym`` space, which is automatically
 added to the list of ``--output-spaces`` if it was not already requested by the user.
-The number of ICA-AROMA components depends on a dimensionality estimate made by 
+The number of ICA-AROMA components depends on a dimensionality estimate made by
 FSL MELODIC.
 For datasets with a very short TR and a large number of timepoints, this may result
 in an unusually high number of components.