revise mentions to mcflirt

Author: oesteban

docs/citing.rst

@@ -100,8 +100,8 @@ we recommend to include in your paper.
 
    <p style="font-style: italic;">
      Functional data was <span class="slicetime_text_true">slice time corrected using
-     <code>3dTshift</code> from AFNI v16.2.07 [11, RRID:SCR_005927]
-     and </span>motion corrected using <code>mcflirt</code> (FSL v5.0.9 [9]).
+     <code>3dTshift</code> (AFNI v16.2.07 [11, RRID:SCR_005927]) and </span>
+     motion-corrected using <code>3dVolreg</code> (AFNI v16.2.07 [11, RRID:SCR_005927]).
      <span class="SDC_text_TOPUP" style="display: none">Distortion correction was performed
      using an implementation of the TOPUP technique [10] using <code>3dQwarp</code> (AFNI v16.2.07 [11]).</span>
      <span class="SDC_text_FUGUE" style="display: none">Distortion correction was performed using fieldmaps
@@ -257,7 +257,7 @@ Other relevant references
   .. [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>`_.
-      
-  .. [Brett2001] Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial Normalization of Brain Images with 
-      Focal Lesions Using Cost Function Masking. NeuroImage 14(2) 
+
+  .. [Brett2001] Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial Normalization of Brain Images with
+      Focal Lesions Using Cost Function Masking. NeuroImage 14(2)
       doi:`10.006/nimg.2001.0845 <https://doi.org/10.1006/nimg.2001.0845>`_.

docs/outputs.rst

@@ -77,8 +77,8 @@ Derivatives related to EPI files are in the ``func`` subfolder.
 Volumetric output spaces include ``T1w`` and ``MNI152NLin2009cAsym`` (default).
 
 - ``*bold_space-<space>_brainmask.nii.gz`` Brain mask for EPI files, calculated by nilearn on the average EPI volume, post-motion correction
-- ``*bold_space-<space>_preproc.nii.gz`` Motion-corrected (using MCFLIRT for estimation and ANTs for interpolation) EPI file
-- (optional) ``*bold_space-<space>_variant-smoothAROMAnonaggr_preproc.nii.gz`` Motion-corrected (using MCFLIRT for estimation and ANTs for interpolation),
+- ``*bold_space-<space>_preproc.nii.gz`` Head-motion corrected EPI file
+- (optional) ``*bold_space-<space>_variant-smoothAROMAnonaggr_preproc.nii.gz`` Head-motion corrected,
   smoothed (6mm), and non-aggressively denoised (using AROMA) EPI file - currently produced only for the ``MNI152NLin2009cAsym`` space
 
 Surface output spaces include ``fsnative`` (full density subject-specific mesh),
@@ -160,7 +160,7 @@ derivative of RMS variance over voxels (or :abbr:`DVARS (D referring to differen
 standardized (``stdDVARS``), non-standardized (``non-stdDVARS``), and voxel-wise standardized (``vx-wisestdDVARS``);
 the ``FrameDisplacement`` is a quantification of the estimated bulk-head motion; ``X``, ``Y``, ``Z``, ``RotX``,
 ``RotY``, ``RotZ`` are the actual 6 rigid-body transform parameters estimated by FMRIPREP;
-the ``NonSteadyStateOutlierXX`` columns indicate non-steady state volumes with a single ``1`` value and ``0`` elsewhere (there 
+the ``NonSteadyStateOutlierXX`` columns indicate non-steady state volumes with a single ``1`` value and ``0`` elsewhere (there
 is one ``NonSteadyStateOutlierXX`` column per outlier/volume); and finally six noise components ``aCompCorXX`` calculated using
 :abbr:`CompCor (Component Based Noise Correction Method)`
 and five noise components ``AROMAaggrCompXX`` if

docs/workflows.rst

@@ -336,7 +336,7 @@ Head-motion estimation
         omp_nthreads=1)
 
 Using the previously :ref:`estimated reference scan <bold_ref>`,
-FSL ``mcflirt`` is used to estimate head-motion.
+AFNI's ``3dVolreg`` is used to estimate head-motion.
 As a result, one rigid-body transform with respect to
 the reference image is written for each :abbr:`BOLD (blood-oxygen level-dependent)`
 time-step.
@@ -546,7 +546,7 @@ Confounds estimation
         metadata={"RepetitionTime": 2.0,
                   "SliceTiming": [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]})
 
-Given a motion-corrected fMRI, a brain mask, ``mcflirt`` movement parameters and a
+Given a motion-corrected fMRI, a brain mask, head-motion parameters and a
 segmentation, the `discover_wf` sub-workflow calculates potential
 confounds per volume.
 

fmriprep/workflows/bold/confounds.py

@@ -46,7 +46,7 @@ def init_bold_confs_wf(mem_gb, metadata, name="bold_confs_wf"):
     #. Region-wise average signal (``CSF``, ``WhiteMatter``, ``GlobalSignal``)
     #. DVARS - standard, nonstandard, and voxel-wise standard variants
        (``stdDVARS``, ``non-stdDVARS``, ``vx-wisestdDVARS``)
-    #. Framewise displacement, based on MCFLIRT motion parameters
+    #. Framewise displacement, based on head-motion parameters
        (``FramewiseDisplacement``)
     #. Temporal CompCor (``tCompCorXX``)
     #. Anatomical CompCor (``aCompCorXX``)