Merge branch 'master' into fix-stc

Author: oesteban

.circleci/config.yml

@@ -388,7 +388,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
-                --debug --write-graph --mem_mb 4096 \
+                --sloppy --write-graph --mem_mb 4096 \
                 --nthreads 2 --anat-only -vv
       - save_cache:
          key: ds005-anat-v9-{{ .Branch }}-{{ epoch }}
@@ -408,7 +408,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
-                --debug --write-graph --use-syn-sdc --mem_mb 4096 \
+                --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
                 --ignore-aroma-denoising-errors --use-aroma \
                 --output-space T1w template fsaverage5 \
                 --template-resampling-grid native \
@@ -435,7 +435,7 @@ jobs:
                 -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
-                --debug --write-graph --use-syn-sdc --mem_mb 4096 \
+                --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
                 --output-space T1w template fsaverage5 \
                 --ignore-aroma-denoising-errors --use-aroma \
                 --template-resampling-grid native \
@@ -517,7 +517,7 @@ jobs:
                 -e FMRIPREP_DEV 1 \
                 --config $PWD/nipype.cfg -w /tmp/ds054/work \
                 /tmp/data/ds054 /tmp/ds054/derivatives participant \
-                --fs-no-reconall --debug --write-graph \
+                --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
          key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
@@ -537,7 +537,7 @@ jobs:
                 -e FMRIPREP_DEV 1 \
                 --config $PWD/nipype.cfg -w /tmp/ds054/work \
                 /tmp/data/ds054 /tmp/ds054/derivatives participant \
-                --fs-no-reconall --debug \
+                --fs-no-reconall --sloppy \
                 --output-space T1w template \
                 --template-resampling-grid 2mm \
                 --mem_mb 4096 --nthreads 2 -vv
@@ -562,7 +562,7 @@ jobs:
                 -e FMRIPREP_DEV 1 \
                 --config $PWD/nipype.cfg -w /tmp/ds054/work \
                 /tmp/data/ds054 /tmp/ds054/derivatives participant \
-                --fs-no-reconall --debug --write-graph \
+                --fs-no-reconall --sloppy --write-graph \
                 --output-space T1w template \
                 --template-resampling-grid 2mm \
                 --reports-only --run-uuid $UUID
@@ -633,7 +633,7 @@ jobs:
                 -e FMRIPREP_DEV 1 \
                 --config $PWD/nipype.cfg -w /tmp/ds210/work \
                 /tmp/data/ds210 /tmp/ds210/derivatives participant \
-                --fs-no-reconall --debug --write-graph \
+                --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
          key: ds210-anat-v4-{{ epoch }}
@@ -651,7 +651,7 @@ jobs:
                 /tmp/data/ds210 /tmp/ds210/derivatives participant \
                 --fs-no-reconall --t2s-coreg --use-syn-sdc \
                 --template-resampling-grid native \
-                --debug --write-graph --mem_mb 4096 --nthreads 2 -vv
+                --sloppy --write-graph --mem_mb 4096 --nthreads 2 -vv
       - run:
           name: Checking outputs of fMRIPrep
           command: |

.zenodo.json

@@ -78,6 +78,11 @@
       "affiliation": "Department of Psychology, Florida International University",
       "orcid": "0000-0001-9813-3167"
     },
+    {
+      "name": "Amlien, Inge K.",
+      "affiliation": "Department of Psychology, University of Oslo",
+      "orcid": "0000-0002-8508-9088"
+    },
     {
       "name": "Liem, Franz",
       "affiliation": "University of Zurich",

fmriprep/cli/run.py

@@ -79,8 +79,6 @@ def get_parser():
                         help='select a specific task to be processed')
 
     g_perfm = parser.add_argument_group('Options to handle performance')
-    g_perfm.add_argument('--debug', action='store_true', default=False,
-                         help='run debug version of workflow')
     g_perfm.add_argument('--nthreads', '--n_cpus', '-n-cpus', action='store', type=int,
                          help='maximum number of threads across all processes')
     g_perfm.add_argument('--omp-nthreads', action='store', type=int, default=0,
@@ -103,6 +101,8 @@ def get_parser():
                               'signal')
     g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
                          help="increases log verbosity for each occurence, debug level is -vvv")
+    g_perfm.add_argument('--debug', action='store_true', default=False,
+                         help='DEPRECATED - Does not do what you want.')
 
     g_conf = parser.add_argument_group('Workflow configuration')
     g_conf.add_argument(
@@ -238,6 +238,8 @@ def get_parser():
                               'the FMRIPREP developers. This information helps to '
                               'improve FMRIPREP and provides an indicator of real '
                               'world usage crucial for obtaining funding.')
+    g_other.add_argument('--sloppy', action='store_true', default=False,
+                         help='Use low-quality tools for speed - TESTING ONLY')
 
     return parser
 
@@ -517,13 +519,15 @@ def build_workflow(opts, retval):
             'Option --output-grid-reference is deprecated, please use '
             '--template-resampling-grid')
         template_out_grid = template_out_grid or opts.output_grid_reference
+    if opts.debug is not None:
+        logger.warning('Option --debug is deprecated and has no effect')
 
     retval['workflow'] = init_fmriprep_wf(
         subject_list=subject_list,
         task_id=opts.task_id,
         run_uuid=run_uuid,
         ignore=opts.ignore,
-        debug=opts.debug,
+        debug=opts.sloppy,
         low_mem=opts.low_mem,
         anat_only=opts.anat_only,
         longitudinal=opts.longitudinal,

fmriprep/interfaces/bids.py

@@ -184,20 +184,35 @@ class DerivativesDataSink(SimpleInterface):
     Saves the `in_file` into a BIDS-Derivatives folder provided
     by `base_directory`, given the input reference `source_file`.
 
+    >>> from pathlib import Path
     >>> import tempfile
     >>> from fmriprep.utils.bids import collect_data
-    >>> tmpdir = tempfile.mkdtemp()
-    >>> tmpfile = os.path.join(tmpdir, 'a_temp_file.nii.gz')
-    >>> open(tmpfile, 'w').close()  # "touch" the file
-    >>> dsink = DerivativesDataSink(base_directory=tmpdir)
-    >>> dsink.inputs.in_file = tmpfile
+    >>> tmpdir = Path(tempfile.mkdtemp())
+    >>> tmpfile = tmpdir / 'a_temp_file.nii.gz'
+    >>> tmpfile.open('w').close()  # "touch" the file
+    >>> dsink = DerivativesDataSink(base_directory=str(tmpdir))
+    >>> dsink.inputs.in_file = str(tmpfile)
     >>> dsink.inputs.source_file = collect_data('ds114', '01')[0]['t1w'][0]
     >>> dsink.inputs.keep_dtype = True
     >>> dsink.inputs.suffix = 'target-mni'
     >>> res = dsink.run()
     >>> res.outputs.out_file  # doctest: +ELLIPSIS
     '.../fmriprep/sub-01/ses-retest/anat/sub-01_ses-retest_target-mni_T1w.nii.gz'
 
+    >>> bids_dir = tmpdir / 'bidsroot' / 'sub-02' / 'ses-noanat' / 'func'
+    >>> bids_dir.mkdir(parents=True, exist_ok=True)
+    >>> tricky_source = bids_dir / 'sub-02_ses-noanat_task-rest_run-01_bold.nii.gz'
+    >>> tricky_source.open('w').close()
+    >>> dsink = DerivativesDataSink(base_directory=str(tmpdir))
+    >>> dsink.inputs.in_file = str(tmpfile)
+    >>> dsink.inputs.source_file = str(tricky_source)
+    >>> dsink.inputs.keep_dtype = True
+    >>> dsink.inputs.desc = 'preproc'
+    >>> res = dsink.run()
+    >>> res.outputs.out_file  # doctest: +ELLIPSIS
+    '.../fmriprep/sub-02/ses-noanat/func/sub-02_ses-noanat_task-rest_run-01_\
+desc-preproc_bold.nii.gz'
+
     """
     input_spec = DerivativesDataSinkInputSpec
     output_spec = DerivativesDataSinkOutputSpec
@@ -221,15 +236,7 @@ def _run_interface(self, runtime):
 
         m = BIDS_NAME.search(src_fname)
 
-        # TODO this quick and dirty modality detection needs to be implemented
-        # correctly
-        mod = 'func'
-        if 'anat' in op.dirname(self.inputs.source_file):
-            mod = 'anat'
-        elif 'dwi' in op.dirname(self.inputs.source_file):
-            mod = 'dwi'
-        elif 'fmap' in op.dirname(self.inputs.source_file):
-            mod = 'fmap'
+        mod = op.basename(op.dirname(self.inputs.source_file))
 
         base_directory = runtime.cwd
         if isdefined(self.inputs.base_directory):