Merge pull request #2781 from effigies/enh/t2s_hist_bounds

ENH: Clip T2* values at 100ms to keep consistent histogram axes

fmriprep/data/reports-spec.yml

@@ -106,7 +106,8 @@ sections:
     subtitle: T2* map
   - bids: {datatype: figures, desc: t2starhist, suffix: bold}
     caption: A histogram of estimated T2* values within the anatomically-derived gray-matter mask
-      shown in the previous plot.
+      shown in the previous plot. Note that values are clipped at 100ms, so any extreme outliers will
+      appear in the 100ms bin.
     static: false
     subtitle: T2* gray-matter values
   - bids: {datatype: figures, desc: flirtnobbr, suffix: bold}

fmriprep/workflows/bold/t2s.py

@@ -31,7 +31,7 @@
 from nipype.interfaces import utility as niu
 
 from ...interfaces.multiecho import T2SMap
-from ...interfaces.maths import Label2Mask
+from ...interfaces.maths import Label2Mask, Clip
 from ...interfaces.reports import LabeledHistogram
 from ... import config
 
@@ -135,7 +135,7 @@ def init_t2s_reporting_wf(name='t2s_reporting_wf'):
     boldref
         reference BOLD file
     label_file
-        an integer label file identifying grey matter with value ``1``
+        an integer label file identifying gray matter with value ``1``
     label_bold_xform
         Affine matrix that maps the label file into alignment with the native
         BOLD space; can be ``"identity"`` if label file is already aligned
@@ -169,6 +169,8 @@ def init_t2s_reporting_wf(name='t2s_reporting_wf'):
 
     gm_mask = pe.Node(Label2Mask(label_val=1), name="gm_mask")
 
+    clip_t2star = pe.Node(Clip(maximum=0.1), name="clip_t2star")
+
     t2s_hist = pe.Node(LabeledHistogram(mapping={1: "Gray matter"}, xlabel='T2* (s)'),
                        name='t2s_hist')
 
@@ -186,7 +188,8 @@ def init_t2s_reporting_wf(name='t2s_reporting_wf'):
         (inputnode, label_tfm, [('label_file', 'input_image'),
                                 ('t2star_file', 'reference_image'),
                                 ('label_bold_xform', 'transforms')]),
-        (inputnode, t2s_hist, [('t2star_file', 'in_file')]),
+        (inputnode, clip_t2star, [('t2star_file', 'in_file')]),
+        (clip_t2star, t2s_hist, [('out_file', 'in_file')]),
         (label_tfm, gm_mask, [('output_image', 'in_file')]),
         (gm_mask, t2s_hist, [('out_file', 'label_file')]),
         (inputnode, t2s_comparison, [('boldref', 'before'),