Merge branch 'master' into enh/3dvolreg

Author: oesteban

.circleci/config.yml

@@ -252,10 +252,12 @@ jobs:
           name: Run fMRIPrep tests
           no_output_timeout: 2h
           command: |
+            mkdir /tmp/data/reports && \
             docker run -ti --rm=false \
               -v /tmp/data:/tmp/data \
               -e FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
               -e FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
+              -e FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
               --entrypoint="py.test" poldracklab/fmriprep:latest \
               /root/src/fmriprep/ \
               --doctest-modules --ignore=/root/src/fmriprep/docs --ignore=setup.py
@@ -284,7 +286,7 @@ jobs:
             fmriprep-docker -i poldracklab/fmriprep:latest --help
             fmriprep-docker -i poldracklab/fmriprep:latest --version
       - store_artifacts:
-          path: /home/circleci/out/tests
+          path: /tmp/data/reports
 
 
   build_docs:

.zenodo.json

@@ -83,6 +83,11 @@
       "affiliation": "Department of Psychology, Stanford University",
       "orcid": "0000-0001-6755-0259"
     },
+    {
+      "name": "Valabregue, Romain",
+      "affiliation": "Cenir, ICM, Paris",
+      "orcid": "0000-0002-1814-9570"
+    },
     {
       "name": "Gorgolewski, Krzysztof J.",
       "affiliation": "Department of Psychology, Stanford University",

CHANGES.rst

@@ -1,3 +1,19 @@
+1.1.7 (September 25, 2018)
+==========================
+
+Several bug fixes. With thanks to Elizabeth Dupre and Romain Vala for
+contributions.
+
+* [FIX] Revert FreeSurfer download URL (#1280) @chrisfilo
+* [FIX] Default to 6 DoF for BOLD-T1w registration (#1286) @effigies
+* [FIX] Only grab sbref images, not metadata (#1285) @effigies
+* [FIX] QwarpPlusMinus renamed source_file to in_file (#1289) @effigies
+* [FIX] Remove long paths from all LTA output files (#1274) @romainVala
+* [ENH] Use single-band reference images when available (#1270) @effigies
+* [DOC] Note GIFTI surface alignment (#1288) @effigies
+* [REF] Split BOLD-T1w registration into calculation/application workflows (#1278) @emdupre
+* [MAINT] Pin pybids and grabbit in Docker build (#1281) @chrisfilo
+
 1.1.6 (September 10, 2018)
 ==========================
 
@@ -8,6 +24,9 @@ Hotfix release.
 1.1.5 (September 06, 2018)
 ==========================
 
+Improved documentation and minor bug fixes. With thanks to Jarod Roland and
+Taylor Salo for contributions.
+
 * [DOC] Replace ``--clearenv`` with correct ``--cleanenv`` flag (#1237) @jarodroland
 * [DOC] De-indent to remove text from code block (#1238) @effigies
 * [TST] Add enhance-and-skullstrip regression tests (#1074) @effigies
@@ -27,13 +46,21 @@ Hotfix release.
 1.1.4 (August 06, 2018)
 =======================
 
+A hotfix release for `#1235
+<https://github.com/poldracklab/fmriprep/issues/1235>`_. Additionally,
+notebooks have been synced with the latest version of that repository.
+
 * [FIX] Verify first word of ``_cmd`` in dependency check (#1236)
 * [DOC] Add two missing references (#1234)
 * [ENH] Allow turning off random seeding for ANTs brain extraction (#919)
 
 1.1.3 (July 30, 2018)
 =====================
 
+This release comes with many updates to the documentation, a more lightweight
+``SignalExtraction``, a new dynamic boilerplate and some new features from
+Nipype.
+
 * [ENH] Use upstream ``afni.TShift`` improvements (#1160)
 * [PIN] Nipype 1.1.1 (65078c9)
 * [ENH] Dynamic citation boilerplate (#1024)

Dockerfile

@@ -114,6 +114,7 @@ RUN conda install -y mkl=2018.0.3 mkl-service;  sync &&\
                      pandas=0.23.0 \
                      libxml2=2.9.4 \
                      libxslt=1.1.29 \
+                     graphviz=2.40.1 \
                      traits=4.6.0; sync &&  \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \
@@ -127,8 +128,7 @@ RUN python -c "from matplotlib import font_manager" && \
 # Installing Ubuntu packages and cleaning up
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
-                    git=1:2.7.4-0ubuntu1 \
-                    graphviz=2.38.0-12ubuntu2 && \
+                    git=1:2.7.4-0ubuntu1 && \
     apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Install latest pandoc
@@ -183,4 +183,3 @@ LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
       org.label-schema.version=$VERSION \
       org.label-schema.schema-version="1.0"
-

docs/workflows.rst

@@ -128,7 +128,7 @@ to be run through ``fmriprep``.
 
 Longitudinal processing
 ~~~~~~~~~~~~~~~~~~~~~~~
-In the case of multiple T1w images (across sessions and/or runs), T1w images are 
+In the case of multiple T1w images (across sessions and/or runs), T1w images are
 merged into a single template image using FreeSurfer's `mri_robust_template`_.
 This template may be *unbiased*, or equidistant from all source images, or
 aligned to the first image (determined lexicographically by session label).
@@ -219,6 +219,12 @@ The ``smoothwm``, ``midthickness``, ``pial`` and ``inflated`` surfaces are also
 converted to GIFTI_ format and adjusted to be compatible with multiple software
 packages, including FreeSurfer and the `Connectome Workbench`_.
 
+.. note::
+    GIFTI surface outputs are aligned to the FreeSurfer T1.mgz image, which
+    may differ from the T1w space in some cases, to maintain compatibility
+    with the FreeSurfer directory.
+    Any measures sampled to the surface take into account any difference in
+    these images.
 
 Refinement of the brain mask
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -376,7 +382,7 @@ T2* Driven Coregistration
 :mod:`fmriprep.workflows.bold.t2s.init_bold_t2s_wf`
 
 .. workflow::
-    :graph2use: colored
+    :graph2use: orig
     :simple_form: yes
 
     from fmriprep.workflows.bold import init_bold_t2s_wf
@@ -389,7 +395,7 @@ T2* Driven Coregistration
 If the ``--t2s-coreg`` command line argument is supplied with multi-echo
 :abbr:`BOLD (blood-oxygen level-dependent)` data, a T2* map is generated.
 This T2* map is then used in place of the :ref:`BOLD reference image <bold_ref>`
-to ref:`register the BOLD series to the T1w image of the same subject <bold_reg>`.
+to :ref:`register the BOLD series to the T1w image <bold_reg>` of the same subject.
 
 Susceptibility Distortion Correction (SDC)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -448,9 +454,9 @@ EPI to T1w registration
         use_bbr=True,
         bold2t1w_dof=9)
 
-The reference :abbr:`EPI (echo-planar imaging)` image of each run is aligned
-by the ``bbregister`` routine to the reconstructed subject using the gray/white
-matter boundary (FreeSurfer's ``?h.white`` surfaces).
+The alignment between the reference :abbr:`EPI (echo-planar imaging)` image
+of each run and the reconstructed subject using the gray/white matter boundary
+(FreeSurfer's ``?h.white`` surfaces) is calculated by the ``bbregister`` routine.
 
 .. figure:: _static/EPIT1Normalization.svg
     :scale: 100%
@@ -459,7 +465,9 @@ matter boundary (FreeSurfer's ``?h.white`` surfaces).
 
 If FreeSurfer processing is disabled, FSL ``flirt`` is run with the
 :abbr:`BBR (boundary-based registration)` cost function, using the
-``fast`` segmentation to establish the gray/white matter boundary. After :abbr:`BBR (boundary-based registration)` is run, the resulting affine transform will be compared to the initial transform found by FLIRT. Excessive deviation will result in rejecting the BBR refinement and accepting the original, affine registration.
+``fast`` segmentation to establish the gray/white matter boundary.
+After :abbr:`BBR (boundary-based registration)` is run, the resulting affine transform will be compared to the initial transform found by FLIRT.
+Excessive deviation will result in rejecting the BBR refinement and accepting the original, affine registration.
 
 EPI to MNI transformation
 ~~~~~~~~~~~~~~~~~~~~~~~~~

fmriprep/__about__.py

@@ -97,7 +97,7 @@
     'grabbit',
     'pybids>=0.6.3',
     'nitime',
-    'nipype>=1.1.1',
+    'nipype>=1.1.3',
     'niworkflows>=0.4.3',
     'statsmodels',
     'seaborn',

fmriprep/cli/run.py

@@ -119,10 +119,9 @@ def get_parser():
              'T2*-driven coregistration. When multi-echo data is provided and this '
              'option is not enabled, standard EPI-T1 coregistration is performed '
              'using the middle echo.')
-    g_conf.add_argument('--bold2t1w-dof', action='store', default=9, choices=[6, 9, 12], type=int,
+    g_conf.add_argument('--bold2t1w-dof', action='store', default=6, choices=[6, 9, 12], type=int,
                         help='Degrees of freedom when registering BOLD to T1w images. '
-                             '9 (rotation, translation, and scaling) is used by '
-                             'default to compensate for field inhomogeneities.')
+                             '6 degrees (rotation and translation) are used by default.')
     g_conf.add_argument(
         '--output-space', required=False, action='store',
         choices=['T1w', 'template', 'fsnative', 'fsaverage', 'fsaverage6', 'fsaverage5'],

fmriprep/interfaces/freesurfer.py

@@ -34,7 +34,9 @@
 )
 from nipype.interfaces import freesurfer as fs
 from nipype.interfaces.base import SimpleInterface
-from nipype.interfaces.freesurfer.preprocess import ConcatenateLTA
+from nipype.interfaces.freesurfer.preprocess import ConcatenateLTA, RobustRegister
+from nipype.interfaces.freesurfer.utils import LTAConvert
+from niworkflows.interfaces.registration import BBRegisterRPT, MRICoregRPT
 
 
 class StructuralReference(fs.RobustTemplate):
@@ -190,7 +192,54 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class PatchedConcatenateLTA(ConcatenateLTA):
+class TruncateLTA(object):
+    """Mixin to ensure that LTA files do not store overly long paths,
+    which lead to segmentation faults when read by FreeSurfer tools.
+
+    See the following issues for discussion:
+
+    * https://github.com/freesurfer/freesurfer/pull/180
+    * https://github.com/poldracklab/fmriprep/issues/768
+    * https://github.com/poldracklab/fmriprep/pull/778
+    * https://github.com/poldracklab/fmriprep/issues/1268
+    * https://github.com/poldracklab/fmriprep/pull/1274
+    """
+
+    # Use a tuple in case some object produces multiple transforms
+    lta_outputs = ('out_lta_file',)
+
+    def _post_run_hook(self, runtime):
+
+        outputs = self._list_outputs()
+
+        for lta_name in self.lta_outputs:
+            lta_file = outputs[lta_name]
+            if not isdefined(lta_file):
+                continue
+
+            with open(lta_file, 'r') as f:
+                lines = f.readlines()
+
+            fixed = False
+            newfile = []
+
+            for line in lines:
+                if line.startswith('filename = ') and len(line.strip("\n")) >= 255:
+                    fixed = True
+                    newfile.append('filename = path_too_long\n')
+                else:
+                    newfile.append(line)
+
+            if fixed:
+                with open(lta_file, 'w') as f:
+                    f.write(''.join(newfile))
+
+        runtime = super(TruncateLTA, self)._post_run_hook(runtime)
+
+        return runtime
+
+
+class PatchedConcatenateLTA(TruncateLTA, ConcatenateLTA):
     """
     A temporarily patched version of ``fs.ConcatenateLTA`` to recover from
     `this bug <https://www.mail-archive.com/[email protected]/msg55520.html>`_
@@ -199,27 +248,30 @@ class PatchedConcatenateLTA(ConcatenateLTA):
 
     The original FMRIPREP's issue is found
     `here <https://github.com/poldracklab/fmriprep/issues/768>`__.
+
+    the fix is now done through mixin with TruncateLTA
     """
+    lta_outputs = ['out_file']
 
-    def _list_outputs(self):
-        outputs = super(PatchedConcatenateLTA, self)._list_outputs()
-
-        with open(outputs['out_file'], 'r') as f:
-            lines = f.readlines()
-
-        fixed = False
-        newfile = []
-        for line in lines:
-            if line.startswith('filename = ') and len(line.strip("\n")) >= 255:
-                fixed = True
-                newfile.append('filename = path_too_long\n')
-            else:
-                newfile.append(line)
-
-        if fixed:
-            with open(outputs['out_file'], 'w') as f:
-                f.write(''.join(newfile))
-        return outputs
+
+class PatchedLTAConvert(TruncateLTA, LTAConvert):
+    """
+    LTAconvert is producing a lta file refer as out_lta
+    truncate filename through mixin TruncateLTA
+    """
+    lta_outputs = ('out_lta',)
+
+
+class PatchedBBRegisterRPT(TruncateLTA, BBRegisterRPT):
+    pass
+
+
+class PatchedMRICoregRPT(TruncateLTA, MRICoregRPT):
+    pass
+
+
+class PatchedRobustRegister(TruncateLTA, RobustRegister):
+    lta_outputs = ('out_reg_file', 'half_source_xfm', 'half_targ_xfm')
 
 
 class RefineBrainMaskInputSpec(BaseInterfaceInputSpec):

fmriprep/workflows/anatomical.py

@@ -49,6 +49,9 @@
     ConcatAffines, RefineBrainMask,
 )
 from ..utils.misc import fix_multi_T1w_source_name, add_suffix
+from ..interfaces.freesurfer import (
+        PatchedLTAConvert as LTAConvert,
+        PatchedRobustRegister as RobustRegister)
 
 TEMPLATE_MAP = {
     'MNI152NLin2009cAsym': 'mni_icbm152_nlin_asym_09c',
@@ -533,7 +536,7 @@ def _get_first(in_list):
     # 2. Reorient template to RAS, if needed (mri_robust_template may set to LIA)
     t1_reorient = pe.Node(image.Reorient(), name='t1_reorient')
 
-    lta_to_fsl = pe.MapNode(fs.utils.LTAConvert(out_fsl=True), iterfield=['in_lta'],
+    lta_to_fsl = pe.MapNode(LTAConvert(out_fsl=True), iterfield=['in_lta'],
                             name='lta_to_fsl')
 
     concat_affines = pe.MapNode(
@@ -813,9 +816,9 @@ def init_surface_recon_wf(omp_nthreads, hires, name='surface_recon_wf'):
 
     skull_strip_extern = pe.Node(FSInjectBrainExtracted(), name='skull_strip_extern')
 
-    fsnative_2_t1_xfm = pe.Node(fs.RobustRegister(auto_sens=True, est_int_scale=True),
+    fsnative_2_t1_xfm = pe.Node(RobustRegister(auto_sens=True, est_int_scale=True),
                                 name='fsnative_2_t1_xfm')
-    t1_2_fsnative_xfm = pe.Node(fs.utils.LTAConvert(out_lta=True, invert=True),
+    t1_2_fsnative_xfm = pe.Node(LTAConvert(out_lta=True, invert=True),
                                 name='t1_2_fsnative_xfm')
 
     autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
@@ -1279,7 +1282,7 @@ def init_anat_derivatives_wf(output_dir, output_spaces, template, freesurfer,
         DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt(template, 'warp')),
         name='ds_t1_mni_warp', run_without_submitting=True)
 
-    lta_2_itk = pe.Node(fs.utils.LTAConvert(out_itk=True), name='lta_2_itk')
+    lta_2_itk = pe.Node(LTAConvert(out_itk=True), name='lta_2_itk')
 
     ds_t1_fsnative = pe.Node(
         DerivativesDataSink(base_directory=output_dir, suffix=suffix_fmt('fsnative', 'affine')),

fmriprep/workflows/bold/__init__.py

@@ -24,7 +24,10 @@
 from .hmc import init_bold_hmc_wf
 from .stc import init_bold_stc_wf
 from .t2s import init_bold_t2s_wf
-from .registration import init_bold_reg_wf
+from .registration import (
+    init_bold_t1_trans_wf,
+    init_bold_reg_wf,
+)
 from .resampling import (
     init_bold_mni_trans_wf,
     init_bold_surf_wf,