[FIX] Count non-steady-state volumes even if sbref is passed

.circleci/config.yml

@@ -354,10 +354,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds005-anat-v10-{{ .Branch }}-{{ epoch }}
-            - ds005-anat-v10-{{ .Branch }}
-            - ds005-anat-v10-master
-            - ds005-anat-v10-
+            - ds005-anat-v11-{{ .Branch }}-{{ epoch }}
+            - ds005-anat-v11-{{ .Branch }}
+            - ds005-anat-v11-master
+            - ds005-anat-v11-
       - run:
           name: Setting up test
           command: |
@@ -391,7 +391,7 @@ jobs:
                 --sloppy --write-graph --mem_mb 4096 \
                 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds005-anat-v10-{{ .Branch }}-{{ epoch }}
+         key: ds005-anat-v11-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds005/work
             - /tmp/ds005/derivatives/fmriprep
@@ -484,10 +484,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds054-anat-v7-{{ .Branch }}-{{ epoch }}
-            - ds054-anat-v7-{{ .Branch }}
-            - ds054-anat-v7-master
-            - ds054-anat-v7-
+            - ds054-anat-v8-{{ .Branch }}-{{ epoch }}
+            - ds054-anat-v8-{{ .Branch }}
+            - ds054-anat-v8-master
+            - ds054-anat-v8-
       - run:
           name: Setting up test
           command: |
@@ -521,7 +521,7 @@ jobs:
                 --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds054-anat-v7-{{ .Branch }}-{{ epoch }}
+         key: ds054-anat-v8-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds054/work
             - /tmp/ds054/derivatives
@@ -602,10 +602,10 @@ jobs:
           at: /tmp
       - restore_cache:
           keys:
-            - ds210-anat-v5-{{ .Branch }}-{{ epoch }}
-            - ds210-anat-v5-{{ .Branch }}
-            - ds210-anat-v5-master
-            - ds210-anat-v5-
+            - ds210-anat-v6-{{ .Branch }}-{{ epoch }}
+            - ds210-anat-v6-{{ .Branch }}
+            - ds210-anat-v6-master
+            - ds210-anat-v6-
       - run:
           name: Setting up test
           command: |
@@ -639,7 +639,7 @@ jobs:
                 --fs-no-reconall --sloppy --write-graph \
                 --mem_mb 4096 --nthreads 2 --anat-only -vv
       - save_cache:
-         key: ds210-anat-v5-{{ .Branch }}-{{ epoch }}
+         key: ds210-anat-v6-{{ .Branch }}-{{ epoch }}
          paths:
             - /tmp/ds210/work
             - /tmp/ds210/derivatives

Dockerfile

@@ -144,11 +144,13 @@ ENV MKL_NUM_THREADS=1 \
 WORKDIR /root/
 
 # Precaching atlases
-ENV CRN_SHARED_DATA /niworkflows_data
+ENV CRN_SHARED_DATA /templateflow
 ADD docker/scripts/get_templates.sh get_templates.sh
 RUN mkdir $CRN_SHARED_DATA && \
     /root/get_templates.sh && \
-    chmod -R a+rX $CRN_SHARED_DATA
+    find $CRN_SHARED_DATA -type d -exec chmod 555 {} \; && \
+    find $CRN_SHARED_DATA -type f -exec chmod 444 {} \; && \
+    chmod +w $CRN_SHARED_DATA
 
 # Installing dev requirements (packages that are not in pypi)
 ADD requirements.txt requirements.txt

docker/scripts/get_templates.sh

@@ -1,13 +1,11 @@
 #!/bin/bash
 
-MNI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705eb594d9001ed622649"
-MNI_SHA256="608b1d609255424d51300e189feacd5ec74b04e244628303e802a6c0b0f9d9db"
-ASYM_09C_TEMPLATE_OLD="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9"
-ASYM_09C_SHA256_OLD="a24699ba0d13f72d0f8934cc211cb80bfd9c9a077b481d9b64295cf5275235a9"
+MNI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5bc984f8ccdb6b0018abb993"
+MNI_SHA256="9bb06ab27d45d21e7f8b2bc2ca27227f081ecb051bbd438a0bfbc56ddc089cac"
 ASYM_09C_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b0dbce20f461a000db8fa3d"
 ASYM_09C_SHA256="2851302474359c2c48995155aadb48b861e5dcf87aefda71af8010f671e8ed66"
-OASIS_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/584123a29ad5a1020913609d"
-OASIS_SHA256="d87300e91346c16f55baf6f54f5f990bc020b61e8d5df9bcc3abb0cc4b943113"
+OASIS_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b0dbce34c28ef0012c7f788"
+OASIS_SHA256="b7202abbca2c69b514a68b8457e3f718a57ccac2c2990fcf7f27ab12f1698645"
 NKI_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5bc3fad82aa873001bc5a553"
 NKI_SHA256="9c08713d067bcf13baa61b01a9495e526b55d1f148d951da01e082679f076fa9"
 OASIS_DKT31_TEMPLATE="https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5b16f17aeca4a80012bd7542"
@@ -30,10 +28,8 @@ GET(){
 }
 
 set -e
-echo "Getting MNI template"
+echo "Getting MNI152Lin template"
 GET "$MNI_TEMPLATE" "$MNI_SHA256"
-echo "Getting (deprecated version of) MNI152NLin2009cAsym template"
-GET "$ASYM_09C_TEMPLATE_OLD" "$ASYM_09C_SHA256_OLD"
 echo "Getting MNI152NLin2009cAsym template"
 GET "$ASYM_09C_TEMPLATE" "$ASYM_09C_SHA256"
 echo "Getting OASIS template"

docs/environment.yml

@@ -21,12 +21,12 @@ dependencies:
 - python-dateutil
 - pydot>=1.2.3
 - cython
-- nipype>=1.1.1
+- nipype>=1.1.5
 
 - pip:
     - sphinx-argparse
     - doctest-ignore-unicode
     - svgutils
     - nitime
     - nilearn
-    - niworkflows==0.4.4
+    - niworkflows==0.5.1

fmriprep/__about__.py

@@ -98,7 +98,7 @@
     'pybids==0.6.5',
     'nitime',
     'nipype>=1.1.5',
-    'niworkflows==0.4.4',
+    'niworkflows==0.5.1',
     'statsmodels',
     'seaborn',
     'indexed_gzip>=0.8.2',

fmriprep/workflows/anatomical.py

@@ -20,8 +20,6 @@
 
 """
 
-import os.path as op
-
 from pkg_resources import resource_filename as pkgr
 
 from nipype.pipeline import engine as pe
@@ -50,12 +48,8 @@
 )
 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',
-    }
+    PatchedLTAConvert as LTAConvert,
+    PatchedRobustRegister as RobustRegister)
 
 
 #  pylint: disable=R0914
@@ -337,10 +331,10 @@ def init_anat_preproc_wf(skull_strip_template, output_spaces, template, debug,
     )
 
     if 'template' in output_spaces:
-        template_str = TEMPLATE_MAP[template]
-        ref_img = op.join(nid.get_dataset(template_str), '1mm_T1.nii.gz')
+        ref_img = str(nid.get_template(template) /
+                      ('tpl-%s_space-MNI_res-01_T1w.nii.gz' % template))
 
-        t1_2_mni.inputs.template = template_str
+        t1_2_mni.inputs.template = template
         mni_mask.inputs.reference_image = ref_img
         mni_seg.inputs.reference_image = ref_img
         mni_tpms.inputs.reference_image = ref_img
@@ -614,7 +608,7 @@ def init_skullstrip_ants_wf(skull_strip_template, debug, omp_nthreads,
             Reportlet visualizing quality of skull-stripping
 
     """
-    from niworkflows.data.getters import get_dataset
+    from niworkflows.data.getters import get_template, TEMPLATE_ALIASES
 
     if skull_strip_template not in ['OASIS', 'NKI']:
         raise ValueError("Unknown skull-stripping template; select from {OASIS, NKI}")
@@ -625,20 +619,10 @@ def init_skullstrip_ants_wf(skull_strip_template, debug, omp_nthreads,
 (ANTs {ants_ver}), using {skullstrip_tpl} as target template.
 """.format(ants_ver=BrainExtraction().version or '<ver>', skullstrip_tpl=skull_strip_template)
 
-    # Grabbing the appropriate template elements
-    template_dir = get_dataset('ants_%s_template_ras' % skull_strip_template.lower())
-    brain_probability_mask = op.join(
-        template_dir, 'T_template0_BrainCerebellumProbabilityMask.nii.gz')
-
-    # TODO: normalize these names so this is not necessary
-    if skull_strip_template == 'OASIS':
-        brain_template = op.join(template_dir, 'T_template0.nii.gz')
-        extraction_registration_mask = op.join(
-            template_dir, 'T_template0_BrainCerebellumRegistrationMask.nii.gz')
-    elif skull_strip_template == 'NKI':
-        brain_template = op.join(template_dir, 'T_template.nii.gz')
-        extraction_registration_mask = op.join(
-            template_dir, 'T_template_BrainCerebellumExtractionMask.nii.gz')
+    # Account for template aliases
+    template_name = TEMPLATE_ALIASES.get(skull_strip_template, skull_strip_template)
+    # Template path
+    template_dir = get_template(template_name)
 
     inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
                         name='inputnode')
@@ -651,9 +635,15 @@ def init_skullstrip_ants_wf(skull_strip_template, debug, omp_nthreads,
                         keep_temporary_files=1, use_random_seeding=not skull_strip_fixed_seed),
         name='t1_skull_strip', n_procs=omp_nthreads)
 
-    t1_skull_strip.inputs.brain_template = brain_template
-    t1_skull_strip.inputs.brain_probability_mask = brain_probability_mask
-    t1_skull_strip.inputs.extraction_registration_mask = extraction_registration_mask
+    # Set appropriate inputs
+    t1_skull_strip.inputs.brain_template = str(
+        template_dir / ('tpl-%s_res-01_T1w.nii.gz' % template_name))
+    t1_skull_strip.inputs.brain_probability_mask = str(
+        template_dir /
+        ('tpl-%s_res-01_class-brainmask_probtissue.nii.gz' % template_name))
+    t1_skull_strip.inputs.extraction_registration_mask = str(
+        template_dir /
+        ('tpl-%s_res-01_label-BrainCerebellumExtraction_roi.nii.gz' % template_name))
 
     workflow.connect([
         (inputnode, t1_skull_strip, [('in_file', 'anatomical_image')]),

fmriprep/workflows/bold/confounds.py

@@ -9,13 +9,12 @@
 .. autofunction:: init_ica_aroma_wf
 
 """
-import os
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, fsl
 from nipype.interfaces.nilearn import SignalExtraction
 from nipype.algorithms import confounds as nac
 
-from niworkflows.data import get_mni_icbm152_linear, get_mni_icbm152_nlin_asym_09c
+from niworkflows.data import get_template
 from niworkflows.interfaces.segmentation import ICA_AROMARPT
 from niworkflows.interfaces.masks import ROIsPlot
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
@@ -358,8 +357,9 @@ def init_carpetplot_wf(mem_gb, metadata, name="bold_carpet_wf"):
     # Warp segmentation into EPI space
     resample_parc = pe.Node(ApplyTransforms(
         float=True,
-        input_image=os.path.join(
-            get_mni_icbm152_nlin_asym_09c(), '1mm_parc.nii.gz'),
+        input_image=str(
+            get_template('MNI152NLin2009cAsym') /
+            'tpl-MNI152NLin2009cAsym_space-MNI_res-01_label-carpet_atlas.nii.gz'),
         dimension=3, default_value=0, interpolation='MultiLabel'),
         name='resample_parc')
 
@@ -531,8 +531,8 @@ def init_ica_aroma_wf(template, metadata, mem_gb, omp_nthreads,
         template=template,
         mem_gb=mem_gb,
         omp_nthreads=omp_nthreads,
-        template_out_grid=os.path.join(get_mni_icbm152_linear(),
-                                       '2mm_T1.nii.gz'),
+        template_out_grid=str(
+            get_template('MNI152Lin') / 'tpl-MNI152Lin_space-MNI_res-02_T1w.nii.gz'),
         use_compression=False,
         use_fieldwarp=use_fieldwarp,
         name='bold_mni_trans_wf'

fmriprep/workflows/bold/resampling.py

@@ -10,14 +10,11 @@
 .. autofunction:: init_bold_preproc_trans_wf
 
 """
-import os.path as op
-
-
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, freesurfer as fs
 from nipype.interfaces.fsl import Split as FSLSplit
 
-from niworkflows import data as nid
+from niworkflows.data import get_template, TEMPLATE_ALIASES
 from niworkflows.interfaces.utils import GenerateSamplingReference
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 
@@ -30,7 +27,6 @@
     PatchedConcatenateLTA as ConcatenateLTA,
     PatchedLTAConvert as LTAConvert
 )
-from ..anatomical import TEMPLATE_MAP
 
 from .util import init_bold_reference_wf
 
@@ -263,8 +259,13 @@ def _aslist(in_value):
 
     gen_ref = pe.Node(GenerateSamplingReference(), name='gen_ref',
                       mem_gb=0.3)  # 256x256x256 * 64 / 8 ~ 150MB)
-    template_str = TEMPLATE_MAP[template]
-    gen_ref.inputs.fixed_image = op.join(nid.get_dataset(template_str), '1mm_T1.nii.gz')
+    # Account for template aliases
+    template_name = TEMPLATE_ALIASES.get(template, template)
+    # Template path
+    template_dir = get_template(template_name)
+
+    gen_ref.inputs.fixed_image = str(
+        template_dir / ('tpl-%s_space-MNI_res-01_T1w.nii.gz' % template_name))
 
     mask_mni_tfm = pe.Node(
         ApplyTransforms(interpolation='MultiLabel', float=True),
@@ -322,11 +323,14 @@ def _aslist(in_value):
             (gen_ref, mask_mni_tfm, [('out_file', 'reference_image')]),
             (gen_ref, bold_to_mni_transform, [('out_file', 'reference_image')]),
         ])
-    elif template_out_grid == '1mm' or template_out_grid == '2mm':
-        mask_mni_tfm.inputs.reference_image = op.join(
-            nid.get_dataset(template_str), '%s_brainmask.nii.gz' % template_out_grid)
-        bold_to_mni_transform.inputs.reference_image = op.join(
-            nid.get_dataset(template_str), '%s_T1.nii.gz' % template_out_grid)
+    elif template_out_grid in ['1mm', '2mm']:
+        res = int(template_out_grid[0])
+        mask_mni_tfm.inputs.reference_image = str(
+            template_dir /
+            ('tpl-%s_space-MNI_res-%02d_brainmask.nii.gz' % (template_name, res)))
+        bold_to_mni_transform.inputs.reference_image = str(
+            template_dir /
+            ('tpl-%s_space-MNI_res-%02d_T1w.nii.gz' % (template_name, res)))
     else:
         mask_mni_tfm.inputs.reference_image = template_out_grid
         bold_to_mni_transform.inputs.reference_image = template_out_grid

requirements.txt

@@ -1,4 +1,4 @@
-niworkflows==0.4.4
+niworkflows==0.5.1
 grabbit==0.2.3
 pybids==0.6.5
 versioneer