Merge pull request #1123 from oesteban/enh/reports-nitpicks

[ENH] Some nit picks of the reports

Author: oesteban

fmriprep/interfaces/reports.py

@@ -44,8 +44,8 @@
 """
 
 ABOUT_TEMPLATE = """\t<ul>
-\t\t<li>FMRIPREP version: {version}</li>
-\t\t<li>FMRIPREP command: <tt>{command}</tt></li>
+\t\t<li>FMRIPrep version: {version}</li>
+\t\t<li>FMRIPrep command: <code>{command}</code></li>
 \t\t<li>Date preprocessed: {date}</li>
 \t</ul>
 </div>
@@ -106,7 +106,7 @@ def _generate_segment(self):
             if recon.cmdline.startswith('echo'):
                 freesurfer_status = 'Pre-existing directory'
             else:
-                freesurfer_status = 'Run by FMRIPREP'
+                freesurfer_status = 'Run by fMRIPrep'
 
         output_spaces = [self.inputs.template if space == 'template' else space
                          for space in self.inputs.output_spaces]
@@ -127,7 +127,7 @@ def _generate_segment(self):
             header = '\t\t<ul class="elem-desc">'
             footer = '\t\t</ul>'
             lines = ['\t\t\t<li>Task: {task_id} ({n_runs:d} run{s})</li>'.format(
-                         task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's')
+                     task_id=task_id, n_runs=n_runs, s='' if n_runs == 1 else 's')
                      for task_id, n_runs in sorted(counts.items())]
             tasks = '\n'.join([header] + lines + [footer])
 
@@ -164,13 +164,16 @@ def _generate_segment(self):
         stc = {True: 'Applied',
                False: 'Not applied',
                'TooShort': 'Skipped (too few volumes)'}[self.inputs.slice_timing]
-        reg = {'FSL': [
-                   'FLIRT with boundary-based registration (BBR) metric - %d dof' % dof,
-                   'FLIRT rigid registration - 6 dof'],
-               'FreeSurfer': [
-                   'FreeSurfer boundary-based registration (bbregister) - %d dof' % dof,
-                   'FreeSurfer mri_coreg - %d dof' % dof],
-               }[self.inputs.registration][self.inputs.fallback]
+        reg = {
+            'FSL': [
+                'FSL <code>flirt</code> with boundary-based registration'
+                ' (BBR) metric - %d dof' % dof,
+                'FSL <code>flirt</code> rigid registration - 6 dof'],
+            'FreeSurfer': [
+                'FreeSurfer <code>bbregister</code> '
+                '(boundary-based registration, BBR) - %d dof' % dof,
+                'FreeSurfer <code>mri_coreg</code> - %d dof' % dof],
+        }[self.inputs.registration][self.inputs.fallback]
         if self.inputs.pe_direction is None:
             pedir = 'MISSING - Assuming Anterior-Posterior'
         else:

fmriprep/viz/config.json

@@ -102,25 +102,25 @@
                 "name": "epi_mean_t1_registration/flirt",
                 "file_pattern": "func/.*_bold_flirt",
                 "title": "EPI to T1 registration",
-                "description": "FLIRT was used to generate transformations from EPI space to T1 Space - BBR refinement rejected"
+                "description": "FSL <code>flirt</code> was used to generate transformations from EPI space to T1 Space - BBR refinement rejected"
             },
             {
                 "name": "epi_mean_t1_registration/coreg",
                 "file_pattern": "func/.*_bold_coreg",
                 "title": "EPI to T1 registration",
-                "description": "mri_coreg (FreeSurfer) was used to generate transformations from EPI space to T1 Space - bbregister refinement rejected"
+                "description": "<code>mri_coreg</code> (FreeSurfer) was used to generate transformations from EPI space to T1 Space - <code>bbregister</code> refinement rejected"
             },
             {
                 "name": "epi_mean_t1_registration/flt_bbr",
                 "file_pattern": "func/.*_bold_flt_bbr",
                 "title": "EPI to T1 registration",
-                "description": "FLIRT was used to generate transformations from EPI space to T1 Space - FAST segmentation used for BBR"
+                "description": "FSL <code>flirt</code> was used to generate transformations from EPI-space to T1w-space - The white matter mask calculated with FSL <code>fast</code> (brain tissue segmentation) was used for BBR"
             },
             {
                 "name": "epi_mean_t1_registration/bbr",
                 "file_pattern": "func/.*_bold_bbr",
                 "title": "EPI to T1 registration",
-                "description": "bbregister was used to generate transformations from EPI space to T1 Space"
+                "description": "<code>bbregister</code> was used to generate transformations from EPI-space to T1w-space"
             },
             {
                 "name": "epi/carpetplot",
@@ -132,7 +132,7 @@
                 "name": "ica_aroma",
                 "file_pattern": "func/.*ica_aroma",
                 "title": "ICA AROMA",
-                "description": "Maps created with maximum intensity projection (glass brain) with a black brain outline. Right hand side of each map: time series (top in seconds), frequency spectrum (bottom in Hertz). Components classified as signal in green; noise in red."
+                "description": "Maps created with maximum intensity projection (glass brain) with a black brain outline. Right hand side of each map: time series (top in seconds), frequency spectrum (bottom in Hertz). Components classified as signal are plotted in green; noise components in red."
             }
         ]
     },