add citation to HCP pipelines, fix grayordinates

Author: oesteban

fmriprep/data/boilerplate.bib

@@ -258,3 +258,15 @@ @article{compcor
     year = 2007
 }
 
+@article{hcppipelines,
+    author = {Glasser, Matthew F. and Sotiropoulos, Stamatios N. and Wilson, J. Anthony and Coalson, Timothy S. and Fischl, Bruce and Andersson, Jesper L. and Xu, Junqian and Jbabdi, Saad and Webster, Matthew and Polimeni, Jonathan R. and Van Essen, David C. and Jenkinson, Mark},
+    doi = {10.1016/j.neuroimage.2013.04.127},
+    issn = {1053-8119},
+    journal = {NeuroImage},
+    pages = {105-124},
+    series = {Mapping the Connectome},
+    title = {The minimal preprocessing pipelines for the Human Connectome Project},
+    url = {http://www.sciencedirect.com/science/article/pii/S1053811913005053},
+    volume = 80,
+    year = 2013
+}

fmriprep/workflows/bold/base.py

@@ -309,8 +309,6 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 effects of other kernels [@lanczos].
 Non-gridded (surface) resamplings were performed using `mri_vol2surf`
 (FreeSurfer).
-*Grayordinates* files, which combine surface-sampled data and
-volume-sampled data, were also generated.
 """
 
     inputnode = pe.Node(niu.IdentityInterface(

fmriprep/workflows/bold/resampling.py

@@ -92,6 +92,8 @@ def init_bold_surf_wf(mem_gb, output_spaces, medial_surface_nan, name='bold_surf
         workflow.__desc__ = """\
 The BOLD time-series, were resampled to surfaces on the following
 spaces: {out_spaces}.
+*Grayordinates* files [@hcppipelines], which combine surface-sampled
+data and volume-sampled data, were also generated.
 """.format(out_spaces=', '.join(['*%s*' % s for s in spaces]))
     inputnode = pe.Node(
         niu.IdentityInterface(fields=['source_file', 't1_preproc', 'subject_id', 'subjects_dir',

fmriprep/workflows/fieldmap/phdiff.py

@@ -61,7 +61,7 @@ def init_phdiff_wf(omp_nthreads, name='phdiff_wf'):
 based on a field map that was co-registered to the BOLD reference,
 using a custom workflow of *fMRIPrep* derived from D. Greve's `epidewarp.fsl`
 [script](http://www.nmr.mgh.harvard.edu/~greve/fbirn/b0/epidewarp.fsl) and
-further improvements of HCP Pipelines.
+further improvements of HCP Pipelines [@hcppipelines].
 """
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['magnitude', 'phasediff']),