Merge remote-tracking branch 'upstream/master' into ref/multiple-output-spaces

Author: oesteban

.circleci/config.yml

@@ -305,7 +305,7 @@ jobs:
           command: |
             cd /home/circleci/src/fmriprep
             if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?docs\]' )" != "" ]]; then
-              echo "Skipping pytest job"
+              echo "Skipping doc building job"
               circleci step halt
             fi
 
@@ -395,6 +395,12 @@ jobs:
                 --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
                 --sloppy --write-graph --mem_mb 4096 \
                 --nthreads 2 --anat-only -vv
+      - run:
+          name: Clean-up after anatomical run
+          command: |
+            rm -rf /tmp/ds005/work/fmriprep_wf/fsdir*
+            rm -rf /tmp/ds005/work/reportlets
+            rm -rf /tmp/ds005/derivatives/fmriprep
       - save_cache:
          key: ds005-anat-v14-{{ .Branch }}-{{ epoch }}
          paths:
@@ -526,6 +532,12 @@ jobs:
                 /tmp/data/ds054 /tmp/ds054/derivatives participant \
                 --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
+      - run:
+          name: Clean-up after anatomical run
+          command: |
+            rm -rf /tmp/ds054/work/fmriprep_wf/fsdir*
+            rm -rf /tmp/ds054/work/reportlets
+            rm -rf /tmp/ds054/derivatives/fmriprep
       - save_cache:
          key: ds054-anat-v12-{{ .Branch }}-{{ epoch }}
          paths:
@@ -644,6 +656,12 @@ jobs:
                 /tmp/data/ds210 /tmp/ds210/derivatives participant \
                 --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
+      - run:
+          name: Clean-up after anatomical run
+          command: |
+            rm -rf /tmp/ds210/work/fmriprep_wf/fsdir*
+            rm -rf /tmp/ds210/work/reportlets
+            rm -rf /tmp/ds210/derivatives/fmriprep
       - save_cache:
          key: ds210-anat-v10-{{ .Branch }}-{{ epoch }}
          paths:

.zenodo.json

@@ -111,6 +111,11 @@
       "affiliation": "Dartmouth College: Hanover, NH, United States",
       "orcid": "0000-0003-3456-2493"
     },
+    {
+      "name": "Rivera-Dompenciel, Adriana",
+      "affiliation": "Neuroscience Program, University of Iowa",
+      "orcid": "0000-0002-3339-4857"
+    },
     {
       "name": "Poldrack, Russell A.",
       "affiliation": "Department of Psychology, Stanford University",

docs/workflows.rst

@@ -78,6 +78,7 @@ T1w/T2w preprocessing
             ('MNI152NLin2009cAsym', {}), ('fsaverage5', {})]),
         reportlets_dir='.',
         skull_strip_template='MNI152NLin2009cAsym',
+        skull_strip_fixed_seed=False,
     )
 
 The anatomical sub-workflow begins by constructing an average image by

fmriprep/__about__.py

@@ -104,8 +104,8 @@
 
 
 LINKS_REQUIRES = [
-    'git+https://github.com/poldracklab/niworkflows.git@'
-    '0863051476f1e6999cd4a028769466e0fc6182fa#egg=niworkflows',
+    'git+https://github.com/oesteban/niworkflows.git@'
+    'c37dda4b7ab28fa8dd6c2136b20721310dd3e91d#egg=niworkflows',
     'git+https://github.com/poldracklab/smriprep.git@'
     'f1cfc37bcdc346549dbf1d037cdade3a3b32d5de#egg=smriprep-0.1.0',
 ]

fmriprep/cli/run.py

@@ -322,9 +322,9 @@ def main():
 
         retcode = p.exitcode or retval.get('return_code', 0)
 
-        bids_dir = retval.get('bids_dir')
+        bids_dir = Path(retval.get('bids_dir'))
         output_dir = Path(retval.get('output_dir'))
-        work_dir = retval.get('work_dir')
+        work_dir = Path(retval.get('work_dir'))
         plugin_settings = retval.get('plugin_settings', None)
         subject_list = retval.get('subject_list', None)
         fmriprep_wf = retval.get('workflow', None)
@@ -372,7 +372,7 @@ def main():
 
             if "Workflow did not execute cleanly" not in str(e):
                 sentry_sdk.capture_exception(e)
-        logger.error('Error: %s', e)
+        logger.critical('fMRIPrep failed: %s', e)
         raise
     else:
         if opts.run_reconall:
@@ -420,8 +420,8 @@ def build_workflow(opts, retval):
     from bids import BIDSLayout
 
     from nipype import logging, config as ncfg
-    from niworkflows.reports import generate_reports
     from niworkflows.utils.bids import collect_participants
+    from niworkflows.reports import generate_reports
     from ..__about__ import __version__
     from ..workflows.base import init_fmriprep_wf
 
@@ -540,7 +540,7 @@ def build_workflow(opts, retval):
             run_uuid = opts.run_uuid
             retval['run_uuid'] = run_uuid
         retval['return_code'] = generate_reports(
-            subject_list, str(output_dir), str(work_dir), run_uuid,
+            subject_list, output_dir, work_dir, run_uuid,
             packagename='fmriprep')
         return retval
 

fmriprep/utils/sentry.py

@@ -1,5 +1,6 @@
-
-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Stripped out routines for Sentry"""
 import os
 from pathlib import Path
 import re

fmriprep/workflows/bold/base.py

@@ -51,6 +51,7 @@
     '164k': 'fsaverage7',
 }
 
+
 def init_func_preproc_wf(
     aroma_melodic_dim,
     bold2t1w_dof,
@@ -675,7 +676,7 @@ def init_func_preproc_wf(
 
         if force_syn and fmaps[0]['suffix'] != 'syn':
             syn_unwarp_report_wf = init_fmap_unwarp_report_wf(
-                suffix='forcedsyn', name='syn_unwarp_report_wf')
+                name='syn_unwarp_report_wf', forcedsyn=True)
             workflow.connect([
                 (inputnode, syn_unwarp_report_wf, [
                     ('t1_seg', 'inputnode.in_seg')]),

fmriprep/workflows/bold/resampling.py

@@ -617,20 +617,20 @@ def init_bold_preproc_report_wf(mem_gb, reportlets_dir, name='bold_preproc_repor
 
     bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                        mem_gb=0.1)
-    bold_rpt_ds = pe.Node(
+    ds_report_bold = pe.Node(
         DerivativesDataSink(base_directory=reportlets_dir, desc='preproc',
-                            keep_dtype=True), name='bold_rpt_ds',
+                            keep_dtype=True), name='ds_report_bold',
         mem_gb=DEFAULT_MEMORY_MIN_GB,
         run_without_submitting=True
     )
 
     workflow.connect([
-        (inputnode, bold_rpt_ds, [('name_source', 'source_file')]),
+        (inputnode, ds_report_bold, [('name_source', 'source_file')]),
         (inputnode, pre_tsnr, [('in_pre', 'in_file')]),
         (inputnode, pos_tsnr, [('in_post', 'in_file')]),
         (pre_tsnr, bold_rpt, [('stddev_file', 'before')]),
         (pos_tsnr, bold_rpt, [('stddev_file', 'after')]),
-        (bold_rpt, bold_rpt_ds, [('out_report', 'in_file')]),
+        (bold_rpt, ds_report_bold, [('out_report', 'in_file')]),
     ])
 
     return workflow

fmriprep/workflows/fieldmap/fmap.py

@@ -64,8 +64,9 @@ def init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf'):
                          name='n4_correct', n_procs=omp_nthreads)
     bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
                   name='bet')
-    ds_fmap_mask = pe.Node(DerivativesDataSink(desc='magnitude', suffix='bold'),
-                           name='ds_report_fmap_mask', run_without_submitting=True)
+    ds_report_fmap_mask = pe.Node(DerivativesDataSink(
+        desc='brain', suffix='mask'), name='ds_report_fmap_mask',
+        run_without_submitting=True)
 
     workflow.connect([
         (inputnode, magmrg, [('magnitude', 'in_files')]),
@@ -74,8 +75,8 @@ def init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf'):
         (n4_correct, bet, [('output_image', 'in_file')]),
         (bet, outputnode, [('mask_file', 'fmap_mask'),
                            ('out_file', 'fmap_ref')]),
-        (inputnode, ds_fmap_mask, [('fieldmap', 'source_file')]),
-        (bet, ds_fmap_mask, [('out_report', 'in_file')]),
+        (inputnode, ds_report_fmap_mask, [('fieldmap', 'source_file')]),
+        (bet, ds_report_fmap_mask, [('out_report', 'in_file')]),
     ])
 
     if fmap_bspline:

fmriprep/workflows/fieldmap/phdiff.py

@@ -83,9 +83,9 @@ def _pick1st(inlist):
                  name='n4', n_procs=omp_nthreads)
     bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
                   name='bet')
-    ds_fmap_mask = pe.Node(DerivativesDataSink(desc='brainmask', suffix='magnitude'),
-                           name='ds_report_fmap_mask',
-                           mem_gb=0.01, run_without_submitting=True)
+    ds_report_fmap_mask = pe.Node(DerivativesDataSink(
+        desc='brain', suffix='mask'), name='ds_report_fmap_mask',
+        mem_gb=0.01, run_without_submitting=True)
     # uses mask from bet; outputs a mask
     # dilate = pe.Node(fsl.maths.MathsCommand(
     #     nan2zeros=True, args='-kernel sphere 5 -dilM'), name='MskDilate')
@@ -128,8 +128,8 @@ def _pick1st(inlist):
         (compfmap, outputnode, [('out_file', 'fmap')]),
         (bet, outputnode, [('mask_file', 'fmap_mask'),
                            ('out_file', 'fmap_ref')]),
-        (inputnode, ds_fmap_mask, [('phasediff', 'source_file')]),
-        (bet, ds_fmap_mask, [('out_report', 'in_file')]),
+        (inputnode, ds_report_fmap_mask, [('phasediff', 'source_file')]),
+        (bet, ds_report_fmap_mask, [('out_report', 'in_file')]),
     ])
 
     return workflow