Update reportlets to indicate FLIRT-BBR if FreeSurfer missing

Author: effigies

fmriprep/viz/config.json

@@ -52,7 +52,13 @@
                 "name": "epi_mean_t1_registration/flt_bbr",
                 "file_pattern": "func/.*_bold_flt_bbr",
                 "title": "EPI",
-                "description": "No SBRef was found so the mean epi was used to generate transformations from EPI space to T1 Space"
+                "description": "No SBRef was found so the mean EPI was used to generate transformations from EPI space to T1 Space - FAST segmentation used for BBR"
+            },
+            {
+                "name": "epi_mean_t1_registration/bbr",
+                "file_pattern": "func/.*_bold_bbr",
+                "title": "EPI",
+                "description": "No SBRef was found so the mean EPI was used to generate transformations from EPI space to T1 Space"
             },
             {
                 "name": "epi/acompcor",
@@ -76,6 +82,12 @@
                 "name": "sbref_t1_registration/flt_bbr",
                 "file_pattern": "func/.*sbref.*flt_bbr",
                 "title": "SBRef to T1 registration",
+                "description": "FreeSurfer surfaces not found - FAST segmentation used for BBR"
+            },
+            {
+                "name": "sbref_t1_registration/bbr",
+                "file_pattern": "func/.*sbref.*bbr",
+                "title": "SBRef to T1 registration",
                 "description": " "
             },
             {

fmriprep/workflows/base.py

@@ -108,7 +108,7 @@ def basic_fmap_sbref_wf(subject_data, settings, name='fMRI_prep'):
     sbref_pre = sbref_preprocess(settings=settings)
 
     # Register SBRef to T1
-    sbref_t1 = ref_epi_t1_registration(reportlet_suffix='sbref_t1_flt_bbr',
+    sbref_t1 = ref_epi_t1_registration(reportlet_suffix='sbref_t1_bbr',
                                        inv_ds_suffix='target-sbref_affine',
                                        settings=settings)
 
@@ -217,7 +217,7 @@ def basic_wf(subject_data, settings, name='fMRI_prep'):
     hmcwf.get_node('inputnode').iterables = ('epi', subject_data['func'])
 
     # mean EPI registration to T1w
-    epi_2_t1 = ref_epi_t1_registration(reportlet_suffix='flt_bbr',
+    epi_2_t1 = ref_epi_t1_registration(reportlet_suffix='bbr',
                                        inv_ds_suffix='target-meanBOLD_affine',
                                        settings=settings)
 

fmriprep/workflows/epi.py

@@ -154,6 +154,7 @@ def apply_fs_transform(fs_2_t1_transform, bbreg_transform):
         )
         flt_bbr.inputs.schedule = op.join(os.getenv('FSLDIR'),
                                           'etc/flirtsch/bbr.sch')
+        reportlet_suffix = reportlet_suffix.replace('bbr', 'flt_bbr')
 
     # make equivalent warp fields
     invt_bbr = pe.Node(fsl.ConvertXFM(invert_xfm=True), name='Flirt_BBR_Inv')