update README

README.rst

@@ -1,26 +1,95 @@
-mriqc
-=====
+mriqc: image quality metrics for quality assessment of MRI
+==========================================================
 
-The mriqc package provides a series of NR (no-reference),
-IQMs (image quality metrics) to used in QAPs (quality
-assessment protocols) for MRI (magnetic resonance imaging).
+This pipeline is developed by `the Poldrack Lab at Stanford University
+<https://poldracklab.stanford.edu>`_ for use at the `Center for Reproducible
+Neuroscience (CRN) <http://reproducibility.stanford.edu>`_, as well as
+for open-source software distribution.
 
 
-Dependencies
-------------
+About
+-----
+
+The package provides a series of image processing workflows to extract and
+compute a series of NR (no-reference), IQMs (image quality metrics) to be 
+used in QAPs (quality assessment protocols) for MRI (magnetic resonance imaging).
+
+This open-source neuroimaging data processing tool is being developed as a
+part of the MRI image analysis and reproducibility platform offered by
+the CRN. This pipeline derives from, and is heavily influenced by, the
+*quality assessment protocols* project [QAP]_.
+
+This tool extracts a series of IQMs from structural and functional MRI data.
+It is also scheduled to add diffusion MRI to the target imaging families.
+
+
+External Dependencies
+---------------------
 
-Make sure you have FSL, N4ITK (released with ANTs), and AFNI installed, and the binaries are available in
-the system's ``$PATH``.
+``mriqc`` is implemented using ``nipype``, but it requires some other neuroimaging
+software tools:
+
+  - `FSL <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>`_.
+  - The N4ITK bias correction tool released with `ANTs <http://stnava.github.io/ANTs/>`_.
+  - `AFNI <https://afni.nimh.nih.gov/>`_.
+
+These tools must be installed and their binaries available in the 
+system's ``$PATH``.
 
 
 Installation
 ------------
 
-Just issue ::
+The ``mriqc`` is packaged and available through the PyPi repository.
+Therefore, the easiest way to install the tool is: ::
 
     pip install mriqc
 
 
-Example command line ::
+
+Execution and the BIDS format
+-----------------------------
+
+The ``mriqc`` workflow takes as principal input the path of the dataset
+that is to be processed.
+The only requirement to the input dataset is that it has a valid `BIDS (Brain
+Imaging Data Structure) <http://bids.neuroimaging.io/>`_ format.
+This can be easily checked online using the 
+`BIDS Validator <http://incf.github.io/bids-validator/>`_.
+
+Example command line: ::
 
     mriqc -i ~/Data/bids_dataset -o out/ -w work/
+
+
+Support and communication
+-------------------------
+
+If you have a problem or would like to ask a question about how to use ``mriqc``,
+please submit a question to NeuroStars.org with an ``mriqc`` tag.
+NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
+
+All previous ``mriqc`` questions are available here:
+http://neurostars.org/t/mriqc/
+
+To participate in the ``mriqc`` development-related discussions please use the 
+following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging
+Please add *[mriqc]* to the subject line when posting on the mailing list.
+
+
+All bugs, concerns and enhancement requests for this software can be submitted here:
+https://github.com/poldracklab/mriqc/issues.
+
+
+Authors
+-------
+
+Oscar Esteban, Krzysztof J. Gorgolewski, Craig A. Moodie, William Triplett.
+Poldrack Lab, Psychology Department, Stanford University,
+and Center for Reproducible Neuroscience, Stanford University.
+
+
+License
+-------
+
+Please see :download:`LICENSE file <./LICENSE.txt>`.

docs/source/measures.rst

@@ -44,15 +44,16 @@ The :abbr:`IQMs (image quality metrics)` computed are as follows:
 |                         |                   | :abbr:`WM (white-matter)`               |
 +-------------------------+-------------------+-----------------------------------------+
 
-Most of these :abbr:`IQMs (image quality metrics)` are migrated or derivated from [QAP]_.
+Most of these :abbr:`IQMs (image quality metrics)` are migrated or derivated from 
+[QAP-measures]_.
 
 
 Functional images (:abbr:`fMRI (functional MRI)`)
 -------------------------------------------------
 
 The :abbr:`IQMs (image quality metrics)` computed are as follows:
 
-#. **efc** Entropy Focus Criterion
+#. :py:func:`~mriqc.qc.anatomical.efc` Entropy Focus Criterion
 #. **fber** - Foreground to Background Energy Ratio
 #. **fwhm** - Full-width half maximum smoothness of the voxels averaged
    across the three coordinate axes, and also for each axis [x,y,x]
@@ -73,5 +74,6 @@ References
 ----------
 
   .. [Tustison2010] Tustison NJ et al., *N4ITK: improved N3 bias correction*, IEEE Trans Med Imag, 29(6):1310-20, 2010. doi:`10.1109/TMI.2010.2046908 <http://dx.doi.org/10.1109/TMI.2010.2046908>`_
-  .. [QAP] `The Quality Assessment Protocols website: Taxonomy of QA Measures
+
+  .. [QAP-measures] `The Quality Assessment Protocols website: Taxonomy of QA Measures
     <http://preprocessed-connectomes-project.github.io/quality-assessment-protocol/#taxonomy-of-qa-measures>`_.