Merge branch 'master' into master

Author: effigies

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

fmriprep/__about__.py

@@ -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',
     'git+https://github.com/rciric/nipype.git@'

fmriprep/workflows/bold/base.py

@@ -348,15 +348,16 @@ 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',
@@ -427,6 +428,10 @@ 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',
@@ -548,8 +553,7 @@ 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'),