Merge pull request #179 from oesteban/fix/178-tpm-label-order

FIX: Make TPMs label ordering in ``io_spec.json`` consistent with workflow
nipreps · Apr 17, 2020 · aa72658 · aa72658
2 parents 076bda9 + 80a99d3
commit aa72658
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/smriprep/data/io_spec.json b/smriprep/data/io_spec.json
@@ -17,7 +17,7 @@
       },
       "tpms": {
         "datatype": "anat",
-        "label": [ "CSF", "WM", "GM"],
+        "label": [ "CSF", "GM", "WM"],
         "suffix": "probseg"
       }
     },

diff --git a/smriprep/workflows/anatomical.py b/smriprep/workflows/anatomical.py
@@ -230,7 +230,6 @@ def init_anat_preproc_wf(
 
         anat_reports_wf.inputs.inputnode.source_file = fix_multi_T1w_source_name(
             [existing_derivatives['t1w_preproc']])
-        anat_reports_wf.inputs.seg_rpt.colors = ['b', 'magenta']
 
         stdselect = pe.Node(KeySelect(
             fields=['std_preproc', 'std_mask'], keys=templates),

diff --git a/smriprep/workflows/outputs.py b/smriprep/workflows/outputs.py
@@ -10,6 +10,8 @@
 
 from ..interfaces import DerivativesDataSink
 
+FSL_FAST_TISSUE_ORDER = ("CSF", "GM", "WM")
+
 
 def init_anat_reports_wf(freesurfer, reportlets_dir,
                          name='anat_reports_wf'):
@@ -27,7 +29,7 @@ def init_anat_reports_wf(freesurfer, reportlets_dir,
     inputnode = pe.Node(niu.IdentityInterface(fields=inputfields),
                         name='inputnode')
 
-    seg_rpt = pe.Node(ROIsPlot(colors=['magenta', 'b'], levels=[1.5, 2.5]),
+    seg_rpt = pe.Node(ROIsPlot(colors=['b', 'magenta'], levels=[1.5, 2.5]),
                       name='seg_rpt')
 
     t1w_conform_check = pe.Node(niu.Function(
@@ -101,7 +103,7 @@ def init_anat_reports_wf(freesurfer, reportlets_dir,
 
 
 def init_anat_derivatives_wf(bids_root, freesurfer, num_t1w, output_dir,
-                             name='anat_derivatives_wf'):
+                             name='anat_derivatives_wf', tpm_labels=FSL_FAST_TISSUE_ORDER):
     """Set up a battery of datasinks to store derivatives in the right location."""
     workflow = Workflow(name=name)
 
@@ -165,7 +167,11 @@ def init_anat_derivatives_wf(bids_root, freesurfer, num_t1w, output_dir,
         DerivativesDataSink(base_directory=output_dir, suffix='probseg',
                             compress=True),
         name='ds_std_tpms', run_without_submitting=True)
-    ds_std_tpms.inputs.extra_values = ['label-CSF', 'label-GM', 'label-WM']
+
+    # CRITICAL: the sequence of labels here (CSF-GM-WM) is that of the output of FSL-FAST
+    #           (intensity mean, per tissue). This order HAS to be matched also by the ``tpms``
+    #           output in the data/io_spec.json file.
+    ds_std_tpms.inputs.extra_values = [f"label-{l}" for l in tpm_labels]
 
     # Transforms
     ds_t1w_tpl_inv_warp = pe.Node(