Merge branch 'master' into circleci_print_skippingDoc

Author: oesteban

.zenodo.json

@@ -106,6 +106,11 @@
       "affiliation": "University College London",
       "orcid": "0000-0002-9699-9052"
     },
+    {
+      "name": "Halchenko, Yaroslav O.",
+      "affiliation": "Dartmouth College: Hanover, NH, United States",
+      "orcid": "0000-0003-3456-2493"
+    },
     {
       "name": "Rivera-Dompenciel, Adriana",
       "affiliation": "Neuroscience Program, University of Iowa",

CONTRIBUTING.md

@@ -111,30 +111,57 @@ is so useful to everyone involved.
 This is now your own unique copy of ``fMRIPrep``.
 Changes here won't effect anyone else's work, so it's a safe space to explore edits to the code!
 
-Make sure to [keep your fork up to date][link_updateupstreamwiki] with the master repository.
+**3. [Clone][link_clone] your forked fMRIPrep repository to your machine/computer**
 
-**3. Make the changes you've discussed, following the [fMRIPrep coding style guide](#fMRIPrep-coding-style-guide).**
+While you can edit files [directly on github][link_githubedit], sometimes the changes
+you want to make will be complex and you will want to use a [text editor][link_texteditor]
+that you have installed on your local machine/computer.
+(One great text editor is [vscode][link_vscode]).
+
+In order to work on the code locally, you must clone your forked repository.
+
+To keep up with changes in the fmriprep repository,
+add the ["upstream" fmriprep repository as a remote][link_addremote]
+to your locally cloned repository.
+
+```Shell
+git remote add upstream https://github.com/poldracklab/fmriprep.git
+```
+
+Make sure to [keep your fork up to date][link_updateupstreamwiki] with the upstream repository.
+
+For example, to update your master branch on your local cloned repository:
+
+```Shell
+git fetch upstream
+git checkout master
+git merge upstream/master
+```
+
+**4. Make the changes you've discussed, following the [fMRIPrep coding style guide](#fMRIPrep-coding-style-guide).**
 
 Try to keep the changes focused.
 If you feel tempted to "branch out" then please make a [new branch][link_branches].
 It can also be helpful to test your changes locally,
 using an [fMRIPrep development environment][link_devel].
+Once you are satisfied with your local changes, [add/commit/push them][link_add_commit_push]
+to the branch on your forked repository.
 
-**4. Submit a [pull request][link_pullrequest].**
+**5. Submit a [pull request][link_pullrequest].**
 
 A member of the development team will review your changes to confirm
 that they can be merged into the main code base.
 
 Pull requests titles should begin with a descriptive prefix:
 
-* ``ENH``: enhancements or new features
-* ``FIX``: bug fixes
-* ``TST``: new or updated tests
-* ``DOC``: new or updated documentation
-* ``STY``: style changes
-* ``REF``: refactoring existing code
-* ``CI``: updates to continous integration infrastructure
-* ``MAINT``: general maintenance
+* ``ENH``: enhancements or new features ([example][enh_ex])
+* ``FIX``: bug fixes ([example][fix_ex])
+* ``TST``: new or updated tests ([example][tst_ex])
+* ``DOC``: new or updated documentation ([example][doc_ex])
+* ``STY``: style changes ([example][sty_ex])
+* ``REF``: refactoring existing code ([example][ref_ex])
+* ``CI``: updates to continous integration infrastructure ([example][ci_ex])
+* ``MAINT``: general maintenance ([example][maint_ex])
 
 For example: `[ENH] Support for SB-reference in multi-band datasets`
 
@@ -229,11 +256,26 @@ You're awesome. :wave::smiley:
 [link_helpwanted]: https://github.com/poldracklab/fmriprep/labels/help%20wanted
 [link_feature]: https://github.com/poldracklab/fmriprep/labels/feature
 
-[link_pullrequest]: https://help.github.com/articles/creating-a-pull-request/
+[link_pullrequest]: https://help.github.com/articles/creating-a-pull-request-from-a-fork
 [link_fork]: https://help.github.com/articles/fork-a-repo/
+[link_clone]: https://help.github.com/articles/cloning-a-repository
+[link_githubedit]: https://help.github.com/articles/editing-files-in-your-repository
+[link_texteditor]: https://en.wikipedia.org/wiki/Text_editor
+[link_vscode]: https://code.visualstudio.com/
+[link_addremote]: https://help.github.com/articles/configuring-a-remote-for-a-fork
 [link_pushpullblog]: https://www.igvita.com/2011/12/19/dont-push-your-pull-requests/
 [link_branches]: https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/
+[link_add_commit_push]: https://help.github.com/articles/adding-a-file-to-a-repository-using-the-command-line
 [link_updateupstreamwiki]: https://help.github.com/articles/syncing-a-fork/
 [link_stemmrolemodels]: https://github.com/KirstieJane/STEMMRoleModels
 [link_zenodo]: https://github.com/poldracklab/fmriprep/blob/master/.zenodo.json
 [link_devel]: https://fmriprep.readthedocs.io/en/latest/contributors.html
+
+[enh_ex]: https://github.com/poldracklab/fmriprep/pull/1508
+[fix_ex]: https://github.com/poldracklab/fmriprep/pull/1378
+[tst_ex]: https://github.com/poldracklab/fmriprep/pull/1098
+[doc_ex]: https://github.com/poldracklab/fmriprep/pull/1515
+[sty_ex]: https://github.com/poldracklab/fmriprep/pull/675
+[ref_ex]: https://github.com/poldracklab/fmriprep/pull/816
+[ci_ex]: https://github.com/poldracklab/fmriprep/pull/1048
+[maint_ex]: https://github.com/poldracklab/fmriprep/pull/1239

docs/environment.yml

@@ -27,7 +27,7 @@ dependencies:
     - doctest-ignore-unicode
     - svgutils
     - nitime
-    - nilearn
+    - nilearn!=0.5.0,!=0.5.1
     - niworkflows<0.9.0a0,>=0.8.1
     - smriprep
     - tedana>=0.0.5

docs/workflows.rst

@@ -126,6 +126,14 @@ in a multiscale, mutual-information based, nonlinear registration scheme.
 In particular, spatial normalization is done using the `ICBM 2009c Nonlinear
 Asymmetric template (1×1×1mm) <http://nist.mni.mcgill.ca/?p=904>`_ [Fonov2011]_.
 
+.. figure:: _static/T1MNINormalization.svg
+    :scale: 100%
+
+    Animation showing T1w to MNI normalization
+
+Cost function masking during spatial normalization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 When processing images from patients with focal brain lesions (e.g. stroke, tumor
 resection), it is possible to provide a lesion mask to be used during spatial
 normalization to MNI-space [Brett2001]_.
@@ -137,11 +145,12 @@ in the same space and resolution as the T1 image, and follow the naming conventi
 (e.g. ``sub-001_T1w_label-lesion_roi.nii.gz``).
 This file should be placed in the ``sub-*/anat`` directory of the BIDS dataset
 to be run through ``fmriprep``.
+Because lesion masks are not currently part of the BIDS specification, it is also necessary to 
+include a ``.bidsignore`` file in the root of your dataset directory. This will prevent 
+`bids-validator <https://github.com/bids-standard/bids-validator#bidsignore>`_ from complaining that your dataset not BIDS valid, which prevents 
+``fmriprep`` from running. Your ``.bidsignore`` file should include the following line::
 
-.. figure:: _static/T1MNINormalization.svg
-    :scale: 100%
-
-    Animation showing T1w to MNI normalization
+*lesion_roi.nii.gz
 
 
 Longitudinal processing

fmriprep/__about__.py

@@ -86,10 +86,10 @@
 REQUIRES = [
     'indexed_gzip>=0.8.8',
     'nibabel>=2.2.1',
-    'nilearn',
+    'nilearn!=0.5.0,!=0.5.1',
     'nipype>=1.1.6',
     'nitime',
-    'niworkflows<0.9.0a0,>=0.8.1',
+    'niworkflows',
     'numpy',
     'pandas',
     'psutil>=5.4',
@@ -104,6 +104,8 @@
 
 
 LINKS_REQUIRES = [
+    'git+https://github.com/poldracklab/niworkflows.git@'
+    'b7d111c8fd36a099c74be5e7671677eedb175533#egg=niworkflows',
     'git+https://github.com/poldracklab/smriprep.git@'
     '423bcc43ab7300177eb3b98da62817b2cad8eb87#egg=smriprep-0.1.0',
 ]

fmriprep/cli/run.py

@@ -786,7 +786,18 @@ def build_workflow(opts, retval):
     boilerplate = retval['workflow'].visit_desc()
 
     if boilerplate:
-        (logs_path / 'CITATION.md').write_text(boilerplate)
+        # To please git-annex users and also to guarantee consistency
+        # among different renderings of the same file, first remove any
+        # existing one
+        citation_files = {
+            ext: logs_path / ('CITATION.%s' % ext)
+            for ext in ('bib', 'tex', 'md', 'html')
+        }
+        for citation_file in citation_files.values():
+            if citation_file.exists() or citation_file.is_symlink():
+                citation_file.unlink()
+
+        citation_files['md'].write_text(boilerplate)
         logger.log(25, 'Works derived from this fMRIPrep execution should '
                    'include the following boilerplate:\n\n%s', boilerplate)
 
@@ -795,8 +806,8 @@ def build_workflow(opts, retval):
                pkgrf('fmriprep', 'data/boilerplate.bib'),
                '--filter', 'pandoc-citeproc',
                '--metadata', 'pagetitle="fMRIPrep citation boilerplate"',
-               str(logs_path / 'CITATION.md'),
-               '-o', str(logs_path / 'CITATION.html')]
+               str(citation_files['md']),
+               '-o', str(citation_files['html'])]
         try:
             check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
@@ -806,16 +817,16 @@ def build_workflow(opts, retval):
         # Generate LaTex file resolving citations
         cmd = ['pandoc', '-s', '--bibliography',
                pkgrf('fmriprep', 'data/boilerplate.bib'),
-               '--natbib', str(logs_path / 'CITATION.md'),
-               '-o', str(logs_path / 'CITATION.tex')]
+               '--natbib', str(citation_files['md']),
+               '-o', str(citation_files['tex'])]
         try:
             check_call(cmd, timeout=10)
         except (FileNotFoundError, CalledProcessError, TimeoutExpired):
             logger.warning('Could not generate CITATION.tex file:\n%s',
                            ' '.join(cmd))
         else:
             copyfile(pkgrf('fmriprep', 'data/boilerplate.bib'),
-                     (logs_path / 'CITATION.bib'))
+                     citation_files['bib'])
 
     return retval
 

fmriprep/workflows/bold/base.py

@@ -338,15 +338,16 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 """
 
     inputnode = pe.Node(niu.IdentityInterface(
-        fields=['bold_file', 'sbref_file', 'subjects_dir', 'subject_id',
+        fields=['bold_file', 'subjects_dir', 'subject_id',
                 't1_preproc', 't1_brain', 't1_mask', 't1_seg', 't1_tpms',
                 't1_aseg', 't1_aparc',
                 't1_2_mni_forward_transform', 't1_2_mni_reverse_transform',
                 't1_2_fsnative_forward_transform', 't1_2_fsnative_reverse_transform']),
         name='inputnode')
     inputnode.inputs.bold_file = bold_file
     if sbref_file is not None:
-        inputnode.inputs.sbref_file = sbref_file
+        from niworkflows.interfaces.images import ValidateImage
+        val_sbref = pe.Node(ValidateImage(in_file=sbref_file), name='val_sbref')
 
     outputnode = pe.Node(niu.IdentityInterface(
         fields=['bold_t1', 'bold_t1_ref', 'bold_mask_t1', 'bold_aseg_t1', 'bold_aparc_t1',
@@ -415,6 +416,10 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
     # Generate a tentative boldref
     bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
+    if sbref_file is not None:
+        workflow.connect([
+            (val_sbref, bold_reference_wf, [('out_file', 'inputnode.sbref_file')]),
+        ])
 
     # Top-level BOLD splitter
     bold_split = pe.Node(FSLSplit(dimension='t'), name='bold_split',
@@ -533,8 +538,7 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
     # MAIN WORKFLOW STRUCTURE #######################################################
     workflow.connect([
         # Generate early reference
-        (inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file'),
-                                        ('sbref_file', 'inputnode.sbref_file')]),
+        (inputnode, bold_reference_wf, [('bold_file', 'inputnode.bold_file')]),
         # BOLD buffer has slice-time corrected if it was run, original otherwise
         (boldbuffer, bold_split, [('bold_file', 'in_file')]),
         # HMC

fmriprep/workflows/bold/util.py

@@ -115,8 +115,6 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, pre_mask=False,
 
     gen_ref = pe.Node(EstimateReferenceImage(), name="gen_ref",
                       mem_gb=1)  # OE: 128x128x128x50 * 64 / 8 ~ 900MB.
-    # Re-run validation; no effect if no sbref; otherwise apply same validation to sbref as bold
-    validate_ref = pe.Node(ValidateImage(), name='validate_ref', mem_gb=DEFAULT_MEMORY_MIN_GB)
     enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(
         omp_nthreads=omp_nthreads, pre_mask=pre_mask)
 
@@ -125,12 +123,11 @@ def init_bold_reference_wf(omp_nthreads, bold_file=None, pre_mask=False,
         (inputnode, validate, [('bold_file', 'in_file')]),
         (inputnode, gen_ref, [('sbref_file', 'sbref_file')]),
         (validate, gen_ref, [('out_file', 'in_file')]),
-        (gen_ref, validate_ref, [('ref_image', 'in_file')]),
-        (validate_ref, enhance_and_skullstrip_bold_wf, [('out_file', 'inputnode.in_file')]),
+        (gen_ref,  enhance_and_skullstrip_bold_wf, [('ref_image', 'inputnode.in_file')]),
         (validate, outputnode, [('out_file', 'bold_file'),
                                 ('out_report', 'validation_report')]),
         (gen_ref, outputnode, [('n_volumes_to_discard', 'skip_vols')]),
-        (validate_ref, outputnode, [('out_file', 'raw_ref_image')]),
+        (gen_ref, outputnode, [('ref_image', 'raw_ref_image')]),
         (enhance_and_skullstrip_bold_wf, outputnode, [
             ('outputnode.bias_corrected_file', 'ref_image'),
             ('outputnode.mask_file', 'bold_mask'),

requirements.txt

@@ -1,3 +1,4 @@
-niworkflows<0.9.0a0,>=0.8.1
+nilearn!=0.5.0,!=0.5.1
+git+https://github.com/poldracklab/niworkflows.git@b7d111c8fd36a099c74be5e7671677eedb175533#egg=niworkflows
 git+https://github.com/poldracklab/smriprep.git@423bcc43ab7300177eb3b98da62817b2cad8eb87#egg=smriprep-0.1.0
 templateflow<0.2.0a0,>=0.1.3