Merge pull request #1113 from danlurie/master

[DOC] Add lesion masking during registration

Author: oesteban

docs/citing.rst

@@ -242,3 +242,7 @@ 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) 
+      doi:`10.006/nimg.2001.0845 <https://doi.org/10.1006/nimg.2001.0845>`_.

docs/workflows.rst

@@ -106,6 +106,18 @@ in a multiscale, mutual-information based, nonlinear registration scheme.
 In particular, spatial normalization is done using the `ICBM 2009c Nonlinear
 Asymmetric template (1×1×1mm) <http://nist.mni.mcgill.ca/?p=904>`_ [Fonov2011]_.
 
+When processing images from patients with focal brain lesions (e.g. stroke, tumor 
+resection), it is possible to provide a lesion mask to be used during spatial 
+normalization to MNI-space [Brett2001]_.
+ANTs will use this mask to minimize warping of healthy tissue into damaged
+areas (or vice-versa). 
+Lesion masks should be binary NIfTI images (damaged areas = 1, everywhere else = 0) 
+in the same space and resolution as the T1 image, and follow the naming convention specified in
+`BIDS Extension Proposal 3: Common Derivatives <https://docs.google.com/document/d/1Wwc4A6Mow4ZPPszDIWfCUCRNstn7d_zzaWPcfcHmgI4/edit#heading=h.9146wuepclkt>`_
+(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``.
+
 .. figure:: _static/T1MNINormalization.svg
     :scale: 100%