Merge pull request #346 from oesteban/rel/0.9.0-fixes

ENH/FIX: Migrate default config to YAML, fix ROIs query.

Author: oesteban

MANIFEST.in

@@ -1,6 +1,10 @@
 # data
 include niworkflows/data/*.json
 include niworkflows/data/tests/work/*
+include niworkflows/reports/figures.json
+include niworkflows/reports/fmriprep.yml
+include niworkflows/reports/report.tpl
+
 
 # misc
 include requirements.txt

niworkflows/__about__.py

@@ -59,6 +59,7 @@
     'packaging',
     'pandas',
     'pybids>=0.7,<0.8',
+    'PyYAML',
     'scikit-image',
     'scipy',
     'seaborn',

niworkflows/reports/core.py

@@ -9,7 +9,6 @@
 
 """
 from pathlib import Path
-import json
 import re
 from itertools import product
 from collections import defaultdict
@@ -196,7 +195,7 @@ class Report(object):
     >>> robj.generate_report()
     0
     >>> len((testdir / 'out' / 'niworkflows' / 'sub-01.html').read_text())
-    17582
+    20862
 
     """
 
@@ -229,11 +228,12 @@ def __init__(self, reportlets_dir, out_dir, run_uuid, config=None,
             self.out_filename = 'sub-{}.html'.format(self.subject_id)
 
         if config is None:
-            config = pkgrf('niworkflows', 'reports/defaultconfig.json')
+            config = pkgrf('niworkflows', 'reports/fmriprep.yml')
         self._load_config(Path(config))
 
     def _load_config(self, config):
-        settings = json.loads(config.read_text())
+        from yaml import load
+        settings = load(config.read_text())
         self.packagename = self.packagename or settings.get('package', None)
 
         if self.packagename is not None:

niworkflows/reports/defaultconfig.json

@@ -0,0 +1,114 @@
+package: niworkflows
+sections:
+- name: Summary
+  reportlets:
+  - bids: {datatype: anat, desc: summary, suffix: T1w}
+- name: Anatomical
+  reportlets:
+  - bids:
+      datatype: anat
+      desc: conform
+      extensions: [.html]
+      suffix: T1w
+  - bids: {datatype: anat, suffix: dseg}
+    caption: This panel shows the template T1-weighted image (if several T1w images
+      were found), with contours delineating the detected brain mask and brain tissue
+      segmentations.
+    subtitle: Brain mask and brain tissue segmentation of the T1w
+  - bids: {datatype: anat, space: .*, suffix: T1w}
+    caption: Spatial normalization of the T1w image to the <code>{space}</code> template.
+    description: Results of nonlinear alignment of the T1w reference one or more template
+      space(s). Hover on the panels with the mouse pointer to transition between both
+      spaces.
+    subtitle: Spatial normalization of the anatomical T1w reference
+  - bids: {datatype: anat, desc: reconall, suffix: T1w}
+    caption: Surfaces (white and pial) reconstructed with FreeSurfer (<code>recon-all</code>)
+      overlaid on the participant's T1w template.
+    subtitle: Surface reconstruction
+- name: Fieldmaps
+  ordering: session
+  reportlets:
+  - bids: {datatype: fmap, desc: brain, suffix: mask}
+    caption: Brain extraction of the magnitude image from the fieldmap
+    subtitle: Skull stripped magnitude image
+- name: Functional
+  ordering: session,task,run
+  reportlets:
+  - bids: {datatype: func, desc: summary, suffix: bold}
+  - bids: {datatype: func, desc: validation, suffix: bold}
+  - bids: {datatype: func, desc: magnitude, suffix: bold}
+    caption: Results of affine coregistration between the magnitude image of the fieldmap
+      and the reference EPI image
+    subtitle: Fieldmap to EPI registration
+  - bids: {datatype: func, desc: fieldmap, suffix: bold}
+    caption: Overlaid on the reference EPI image
+    subtitle: Fieldmap
+  - bids: {datatype: func, desc: sdc, suffix: bold}
+    caption: Results of performing susceptibility distortion correction (SDC) on the
+      EPI
+    subtitle: Susceptibility distortion correction
+  - bids: {datatype: func, desc: forcedsyn, suffix: bold}
+    caption: The dataset contained some fieldmap information, but the argument <code>--force-syn</code>
+      was used. The higher-priority SDC method was used. Here, we show the results
+      of performing SyN-based SDC on the EPI for comparison.
+    subtitle: Experimental fieldmap-less susceptibility distortion correction
+  - bids: {datatype: func, desc: rois, suffix: bold}
+    caption: Brain mask calculated on the BOLD signal (red contour), along with the
+      masks used for a/tCompCor.<br />The aCompCor mask (magenta contour) is a conservative
+      CSF and white-matter mask for extracting physiological and movement confounds.
+      <br />The fCompCor mask (blue contour) contains the top 5% most variable voxels
+      within a heavily-eroded brain-mask.
+    subtitle: ROIs in BOLD space
+  - bids:
+      datatype: func
+      desc: '[at]compcor'
+      extensions: [.html]
+      suffix: bold
+  - bids: {datatype: func, desc: flirtnobbr, suffix: bold}
+    caption: FSL <code>flirt</code> was used to generate transformations from EPI
+      space to T1 Space - BBR refinement rejected. Note that Nearest Neighbor interpolation
+      is used in the reportlets in order to highlight potential spin-history and other
+      artifacts, whereas final images are resampled using Lanczos interpolation.
+    subtitle: EPI to T1 registration
+  - bids: {datatype: func, desc: coreg, suffix: bold}
+    caption: <code>mri_coreg</code> (FreeSurfer) was used to generate transformations
+      from EPI space to T1 Space - <code>bbregister</code> refinement rejected. Note
+      that Nearest Neighbor interpolation is used in the reportlets in order to highlight
+      potential spin-history and other artifacts, whereas final images are resampled
+      using Lanczos interpolation.
+    subtitle: EPI to T1 registration
+  - bids: {datatype: func, desc: flirtbbr, suffix: bold}
+    caption: 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. Note that Nearest Neighbor interpolation
+      is used in the reportlets in order to highlight potential spin-history and other
+      artifacts, whereas final images are resampled using Lanczos interpolation.
+    subtitle: EPI to T1 registration
+  - bids: {datatype: func, desc: bbregister, suffix: bold}
+    caption: <code>bbregister</code> was used to generate transformations from EPI-space
+      to T1w-space. Note that Nearest Neighbor interpolation is used in the reportlets
+      in order to highlight potential spin-history and other artifacts, whereas final
+      images are resampled using Lanczos interpolation.
+    subtitle: EPI to T1 registration
+  - bids: {datatype: func, desc: carpetplot, suffix: bold}
+    caption: Summary statistics are plotted, which may reveal trends or artifacts
+      in the BOLD data. Global signals calculated within the whole-brain (GS), within
+      the white-matter (WM) and within cerebro-spinal fluid (CSF) show the mean BOLD
+      signal in their corresponding masks. DVARS and FD show the standardized DVARS
+      and framewise-displacement measures for each time point.<br />A carpet plot
+      shows the time series for all voxels within the brain mask. Voxels are grouped
+      into cortical (blue), and subcortical (orange) gray matter, cerebellum (green)
+      and white matter and CSF (red), indicated by the color map on the left-hand
+      side.
+    subtitle: BOLD Summary
+  - bids: {datatype: func, desc: aroma, suffix: bold}
+    caption: |
+      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.
+    subtitle: ICA Components classified by AROMA
+- name: About
+  reportlets:
+  - bids: {datatype: anat, desc: about, suffix: T1w}
+template_path: report.tpl

niworkflows/reports/fmriprep.yml

@@ -33,8 +33,8 @@ def main():
         'niworkflows': [
             'data/t1-mni_registration*.json',
             'data/bold-mni_registration*.json',
-            'reports/defaultconfig.json',
             'reports/figures.json',
+            'reports/fmriprep.yml',
             'reports/report.tpl',
         ]}