Merge pull request #1527 from oesteban/pin/niworkflows-0.8

REL: 1.3.1

Author: oesteban

.circleci/config.yml

@@ -389,7 +389,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --sloppy --write-graph --mem_mb 4096 \
@@ -408,7 +408,7 @@ jobs:
             sudo setfacl -d -m group:$(id -gn):rwx /tmp/ds005/work && \
                 sudo setfacl -m group:$(id -gn):rwx /tmp/ds005/work
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work \
                 /tmp/data/ds005 /tmp/ds005/derivatives participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \
@@ -437,7 +437,7 @@ jobs:
           command: |
             rm /tmp/data/ds005/sub-01/func/*_run-01_*
             fmriprep-docker -i poldracklab/fmriprep:latest \
-                -e FMRIPREP_DEV 1 \
+                -e FMRIPREP_DEV 1 -u $(id -u) \
                 --config $PWD/nipype.cfg -w /tmp/ds005/work_partial \
                 /tmp/data/ds005 /tmp/ds005/derivatives_partial participant \
                 --sloppy --write-graph --use-syn-sdc --mem_mb 4096 \

CHANGES.rst

@@ -1,15 +1,32 @@
+1.3.0.post3 (March 1, 2019)
+===========================
+
+Hotfix release intended for Docker users, smoothing the experience of TemplateFlow
+when using the ``-u UID`` flag is necessary.
+
+* [FIX] Orientation problem with niworkflows<0.7.2 (poldracklab/niworkflows#312) @effigies
+* [ENH] TemplateFlow + ``docker run -u ...`` (#1525) @oesteban
+* [ENH] Include repetition time in functional summary (#1508) @wiheto
+* [FIX] Do not crash if all aroma components are classified as noise (#1467) @jdkent
+
+1.3.0.post2 (February 14, 2019)
+===============================
+
+Hotfix release intended for Singularity users, amending the previous iteration
+that didn't fix the problem (#1510) @effigies.
+
 1.3.0.post1 (February 8, 2019)
 ==============================
 
-Hotfix release intended for Singularity users. For further detail, please see 
+Hotfix release intended for Singularity users. For further detail, please see
 `#1500 <https://github.com/poldracklab/fmriprep/issues/1500>`__.
 
 1.3.0 (February 7, 2019)
 ========================
 
 We start the 1.3.x series including a few bugfixes, housekeeping duty and a refactors
 to leverage `sMRIPrep <https://github.com/poldracklab/smriprep>`__ (which is a fork of
-fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and 
+fMRIPrep's anatomical workflow), pybids>=0.7 for querying dataset, and
 `TemplateFlow <https://github.com/templateflow>`__ for handling standard spaces.
 
 * [FIX] Bad ``fsnative`` replacement in CIfTI workflow (#1476) @oesteban
@@ -71,7 +88,7 @@ Hotfix release.
 1.2.4 (December 3, 2018)
 ========================
 
-Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates 
+Bugfixes, an additional iteration over Sentry reporting and some relevant ME-EPI updates
 (with thanks to @emdupre).
 
 * [ENH] Update ME-EPI workflow to create optimal combination (#1263) @emdupre
@@ -153,7 +170,7 @@ With many thanks to Ali Cohen, James Kent, Inge Amlien, Sebastian Urchs, and Zhi
 * [TST] Add heavily-nonuniform boldrefs for regression tests (#1329) @oesteban
 * [TST] Fix expectations for CIFTI outputs & ds005 (#1344) @oesteban
 * [MAINT] Ignore project settings files from popular python/code editors (#1336) @jdkent
-* [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies 
+* [CI] Deploy poldracklab/fmriprep:unstable tracking master (#1307) @effigies
 
 1.1.8 (October 4, 2018)
 =======================

Dockerfile

@@ -2,7 +2,7 @@
 FROM ubuntu:xenial-20161213
 
 # Pre-cache neurodebian key
-COPY docker/files/neurodebian.gpg /root/.neurodebian.gpg
+COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
 
 # Prepare environment
 RUN apt-get update && \
@@ -67,7 +67,7 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
 
 # Installing Neurodebian packages (FSL, AFNI, git)
 RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
-    apt-key add /root/.neurodebian.gpg && \
+    apt-key add /usr/local/etc/neurodebian.gpg && \
     (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
 
 RUN apt-get update && \
@@ -98,6 +98,11 @@ RUN mkdir -p $ANTSPATH && \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH:$PATH
 
+# Create a shared $HOME directory
+RUN useradd -m -s /bin/bash -G users fmriprep
+WORKDIR /home/fmriprep
+ENV HOME="/home/fmriprep"
+
 # Installing SVGO
 RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
 RUN apt-get install -y nodejs
@@ -142,41 +147,30 @@ RUN conda install -y python=3.7.1 \
                      zlib; sync && \
     chmod -R a+rX /usr/local/miniconda; sync && \
     chmod +x /usr/local/miniconda/bin/*; sync && \
-    conda clean --all -y; sync && \
+    conda build purge-all; sync && \
     conda clean -tipsy && sync
 
-# Precaching fonts, set 'Agg' as default backend for matplotlib
-RUN python -c "from matplotlib import font_manager" && \
-    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
-RUN pip install "datalad==0.10.0" && \
-    rm -rf ~/.cache/pip
-
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1
 
+# Precaching fonts, set 'Agg' as default backend for matplotlib
+RUN python -c "from matplotlib import font_manager" && \
+    sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
 # Precaching atlases
-RUN git config --global user.name "fMRIPrep User" && \
-    git config --global user.email "[email protected]"
-ENV TEMPLATEFLOW_HOME="/opt/templateflow"
-WORKDIR /opt
-RUN datalad install -r https://github.com/templateflow/templateflow.git
-RUN datalad get $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/* \
-                $TEMPLATEFLOW_HOME/tpl-MNI152Lin/* \
-                $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/* \
-                $TEMPLATEFLOW_HOME/tpl-NKI/*
-RUN git -C $TEMPLATEFLOW_HOME config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-MNI152Lin config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs config annex.merge-annex-branches false && \
-    git -C $TEMPLATEFLOW_HOME/tpl-NKI config annex.merge-annex-branches false
+RUN pip install --no-cache-dir "templateflow>=0.1.0,<0.2.0a0" && \
+    python -c "from templateflow import api as tfapi; \
+               tfapi.get('MNI152Lin'); \
+               tfapi.get('MNI152NLin2009cAsym'); \
+               tfapi.get('OASIS30ANTs'); \
+               tfapi.get('NKI');"
 
 # Installing dev requirements (packages that are not in pypi)
 WORKDIR /src/
 COPY requirements.txt requirements.txt
-RUN pip install -r requirements.txt && \
-    rm -rf ~/.cache/pip
+RUN pip install --no-cache-dir -r requirements.txt
 
 # Installing FMRIPREP
 COPY . /src/fmriprep
@@ -185,13 +179,15 @@ ARG VERSION
 RUN echo "${VERSION}" > /src/fmriprep/fmriprep/VERSION && \
     echo "include fmriprep/VERSION" >> /src/fmriprep/MANIFEST.in && \
     cd /src/fmriprep && \
-    pip install .[all] && \
-    rm -rf ~/.cache/pip
+    pip install --no-cache-dir .[all]
 
 RUN install -m 0755 \
     /src/fmriprep/scripts/generate_reference_mask.py \
     /usr/local/bin/generate_reference_mask
 
+RUN find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} +
+
 ENV IS_DOCKER_8395080871=1
 
 RUN ldconfig

fmriprep/__about__.py

@@ -88,18 +88,17 @@
     'nibabel>=2.2.1',
     'nilearn',
     'nipype>=1.1.6',
-    'nitime',
-    'niworkflows>=0.7.2,<0.8.0a0',
+    'niworkflows<0.9.0a0,>=0.8.0',
     'numpy',
     'pandas',
     'psutil>=5.4',
-    'pybids>=0.7.0,<0.8.0a0',
+    'pybids<0.8.0a0,>=0.7.1',
     'pyyaml',
     'scikit-image',
-    'smriprep>=0.0.5,<0.1.0a0',
+    'smriprep<0.2.0a0,>=0.1.0',
     'statsmodels',
     'tedana>=0.0.5',
-    'templateflow>=0.0.4',
+    'templateflow<0.2.0a0,>=0.1.0',
 ]
 
 

fmriprep/workflows/bold/confounds.py

@@ -360,8 +360,9 @@ 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=get_template('MNI152NLin2009cAsym',
-                                 '_res-01_desc-carpet_dseg.nii.gz'),
+        input_image=str(get_template(
+            'MNI152NLin2009cAsym', resolution=1, desc='carpet',
+            suffix='dseg', extensions=['.nii', '.nii.gz'])),
         dimension=3, default_value=0, interpolation='MultiLabel'),
         name='resample_parc')
 
@@ -536,7 +537,9 @@ def init_ica_aroma_wf(template, metadata, mem_gb, omp_nthreads,
         freesurfer=False,
         mem_gb=mem_gb,
         omp_nthreads=omp_nthreads,
-        template_out_grid=get_template('MNI152Lin', 'res-02_T1w.nii.gz'),
+        template_out_grid=str(get_template(
+            'MNI152Lin', resolution=2, desc=None, suffix='T1w',
+            extensions=['.nii', '.nii.gz'])),
         use_compression=False,
         use_fieldwarp=use_fieldwarp,
         name='bold_mni_trans_wf'

fmriprep/workflows/bold/resampling.py

@@ -282,7 +282,9 @@ def _aslist(in_value):
 
     gen_ref = pe.Node(GenerateSamplingReference(), name='gen_ref',
                       mem_gb=0.3)  # 256x256x256 * 64 / 8 ~ 150MB)
-    gen_ref.inputs.fixed_image = get_template(template, '_res-01_T1w.nii.gz')
+    gen_ref.inputs.fixed_image = str(get_template(
+        template, resolution=1, desc=None, suffix='T1w',
+        extensions=['.nii', '.nii.gz']))
 
     mask_mni_tfm = pe.Node(
         ApplyTransforms(interpolation='MultiLabel', float=True),
@@ -342,10 +344,11 @@ def _aslist(in_value):
         ])
     elif template_out_grid in ['1mm', '2mm']:
         res = int(template_out_grid[0])
-        mask_mni_tfm.inputs.reference_image = get_template(
-            template, '_res-%02d_desc-brain_mask.nii.gz' % res)
-        bold_to_mni_transform.inputs.reference_image = get_template(
-            template, '_res-%02d_T1w.nii.gz' % res)
+        mask_mni_tfm.inputs.reference_image = str(get_template(
+            template, resolution=res, desc='brain', suffix='mask'))
+        bold_to_mni_transform.inputs.reference_image = str(get_template(
+            template, resolution=res, desc=None, suffix='T1w',
+            extensions=['.nii', '.nii.gz']))
     else:
         mask_mni_tfm.inputs.reference_image = template_out_grid
         bold_to_mni_transform.inputs.reference_image = template_out_grid
@@ -373,11 +376,13 @@ def _aslist(in_value):
                 (gen_ref, aparc_mni_tfm, [('out_file', 'reference_image')]),
             ])
         elif template_out_grid in ['1mm', '2mm']:
-            res = int(template_out_grid[0])
-            aseg_mni_tfm.inputs.reference_image = get_template(
-                template, '_res-%02d_desc-brain_mask.nii.gz' % res)
-            aparc_mni_tfm.inputs.reference_image = get_template(
-                template, '_res-%02d_desc-brain_mask.nii.gz' % res)
+            entities = {'resolution': int(template_out_grid[0]),
+                        'desc': 'brain', 'suffix': 'mask',
+                        'extensions': ['.nii', '.nii.gz']}
+            aseg_mni_tfm.inputs.reference_image = str(
+                get_template(template, **entities))
+            aparc_mni_tfm.inputs.reference_image = str(
+                get_template(template, **entities))
         else:
             aseg_mni_tfm.inputs.reference_image = template_out_grid
             aparc_mni_tfm.inputs.reference_image = template_out_grid

fmriprep/workflows/bold/util.py

@@ -275,8 +275,10 @@ def init_enhance_and_skullstrip_bold_wf(
     apply_mask = pe.Node(fsl.ApplyMask(), name='apply_mask')
 
     if not pre_mask:
-        bold_template = get_template('MNI152NLin2009cAsym', 'res-02_desc-fMRIPrep_boldref.nii.gz')
-        brain_mask = get_template('MNI152NLin2009cAsym', 'res-02_desc-brain_mask.nii.gz')
+        bold_template = get_template(
+            'MNI152NLin2009cAsym', resolution=2, desc='fMRIPrep', suffix='boldref')
+        brain_mask = get_template(
+            'MNI152NLin2009cAsym', resolution=2, desc='brain', suffix='mask')
 
         # Initialize transforms with antsAI
         init_aff = pe.Node(AI(

requirements.txt

@@ -1,4 +1 @@
-pybids>=0.7.0,<0.8.0a0
-niworkflows>=0.7.2,<0.8.0a0
-smriprep>=0.0.5,<0.1.0a0
-templateflow>=0.0.4
+smriprep<0.2.0a0,>=0.1.0