Merge pull request #49 from akeshavan/new_fsl

New fsl

Author: richford

dmriprep/cli.py

@@ -7,6 +7,12 @@
 from . import io
 from .data import get_dataset
 import os
+import warnings
+
+# Filter warnings that are visible whenever you import another package that
+# was compiled against an older numpy than is installed.
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
+warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
 
 
 @click.command()
@@ -72,8 +78,26 @@ def main(participant_label, bids_dir, output_dir,
 @click.command()
 @click.argument('output_dir',
                 )
-def data(output_dir):
-    get_dataset(os.path.abspath(output_dir))
+@click.option('--subject', help="subject id to download (will choose 1 subject if not specified",
+              default="sub-NDARBA507GCT")
+@click.option('--study', help="which study to download. Right now we only support the HBN dataset",
+              default="HBN")
+def data(output_dir, study="HBN", subject="sub-NDARBA507GCT"):
+    """
+    Download dwi raw data in BIDS format from public datasets
+
+    :param output_dir: A directory to write files to
+    :param study: A study name, right now we only support 'HBN'
+    :param subject: A subject from the study, starting with 'sub-'
+    :return: None
+    """
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    if study.upper() != 'HBN':
+        raise NotImplementedError('We only support data downloads from the HBN dataset right now.')
+
+    get_dataset(os.path.abspath(output_dir), source=study.upper(), subject_id=subject)
     print('done')
 
 

dmriprep/data.py

@@ -20,15 +20,14 @@
 mod_logger = logging.getLogger(__name__)
 
 
-def get_dataset(output_dir, source='HBN'):
+def get_dataset(output_dir, source='HBN', subject_id='sub-NDARBA507GCT'):
     if source in ['HBN']:
-        get_hbn_data(output_dir)
+        get_hbn_data(output_dir, subject_id)
     else:
         raise ValueError('Invalid dataset source')
 
 
-def get_hbn_data(output_dir):
-    subject_id = 'sub-NDARBA507GCT'
+def get_hbn_data(output_dir, subject_id):
     hbn_study = HBN(subjects=subject_id)
     subject = hbn_study.subjects[0]
     subject.download(directory=output_dir)

dmriprep/run.py

@@ -1,4 +1,5 @@
 import os.path as op
+import os
 from shutil import copyfile
 
 
@@ -357,6 +358,10 @@ def get_dmriprep_pe_workflow():
 
     eddy = prep.get_node('fsl_eddy')
     eddy.inputs.repol = True
+    eddy.inputs.cnr_maps = True
+    eddy.inputs.residuals = True
+    import multiprocessing
+    eddy.inputs.num_threads = multiprocessing.cpu_count()
 
     def id_outliers_fn(outlier_report, threshold, dwi_file):
         """Get list of scans that exceed threshold for number of outliers
@@ -669,6 +674,10 @@ def binarize_aparc(aparc_aseg):
                datasink, "dmriprep.qc.@eddyparamsshellalign")
     wf.connect(prep, "fsl_eddy.out_parameter",
                datasink, "dmriprep.qc.@eddyparams")
+    wf.connect(prep, "fsl_eddy.out_cnr_maps",
+               datasink, "dmriprep.qc.@eddycndr")
+    wf.connect(prep, "fsl_eddy.out_residuals",
+               datasink, "dmriprep.qc.@eddyresid")
 
     # the file that told us which volumes to trop
     wf.connect(id_outliers_node, "outpath", datasink, "dmriprep.qc.@droppedscans")

docker/Dockerfile

@@ -39,8 +39,8 @@ RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
 
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
-ENV FSLDIR="/opt/fsl-5.0.11" \
-    PATH="/opt/fsl-5.0.11/bin:$PATH"
+ENV FSLDIR="/opt/fsl-6.0.0" \
+    PATH="/opt/fsl-6.0.0/bin:$PATH"
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
            bc \
@@ -63,15 +63,15 @@ RUN apt-get update -qq \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && echo "Downloading FSL ..." \
-    && mkdir -p /opt/fsl-5.0.11 \
-    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-centos6_64.tar.gz \
-    | tar -xz -C /opt/fsl-5.0.11 --strip-components 1 \
+    && mkdir -p /opt/fsl-6.0.0 \
+    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-centos6_64.tar.gz \
+    | tar -xz -C /opt/fsl-6.0.0 --strip-components 1 \
     && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
     && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
     && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
     && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
     && echo "Installing FSL conda environment ..." \
-    && bash /opt/fsl-5.0.11/etc/fslconf/fslpython_install.sh -f /opt/fsl-5.0.11
+    && bash /opt/fsl-6.0.0/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.0
 
 ENV CONDA_DIR="/opt/miniconda-latest" \
     PATH="/opt/miniconda-latest/bin:$PATH"
@@ -132,12 +132,13 @@ RUN apt-get update -qq \
 
 COPY ./license.txt /opt/freesurfer-6.0.0/license.txt
 
+#&& sync && conda clean -tipsy && sync
+
 ADD environment.yml environment.yml
-RUN apt-get update && apt-get install -y git gcc
+RUN apt-get update && apt-get install -y git gcc libopenblas-base
 RUN conda env create -f environment.yml
 
-#&& sync && conda clean -tipsy && sync
-
+ENV LD_LIBRARY_PATH=/usr/lib/openblas-base/
 
 RUN sed -i '$isource activate dmriprep' $ND_ENTRYPOINT
 
@@ -152,7 +153,7 @@ RUN echo '{ \
     \n    [ \
     \n      "fsl", \
     \n      { \
-    \n        "version": "5.0.11" \
+    \n        "version": "6.0.0" \
     \n      } \
     \n    ], \
     \n    [ \

docker/environment.yml

@@ -11,6 +11,6 @@ dependencies:
    - pandas
    - tqdm
    - pip:
-     - "--editable=git+https://github.com/nipy/nipype@fa0a101fec2d010dcb68910000f66d7c64e5d03e#egg=nipype"
+     - "--editable=git+https://github.com/nipy/nipype@35b58cdb59a900430f4b9639e220c8408341805d#egg=nipype"
      - bids
      - duecredit

kubernetes/delete_cluster.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+gcloud container clusters delete dmriprep --zone=us-west1-a

kubernetes/delete_job.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+kubectl delete -f run_dmriprep.yml

kubernetes/docker/build_tag_push.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+docker build -t dmriprep:kube1 -f dockerfile-dmriprep-kube1 .
+docker tag dmriprep:kube1 gcr.io/dmriprep/dmriprep:kube1
+docker push gcr.io/dmriprep/dmriprep:kube1

kubernetes/docker/dmriprep_all.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+mkdir inputs
+mkdir outputs
+dmriprep-data --subject $1 $PWD/inputs/
+dmriprep $PWD/inputs $PWD/outputs
+dmriprep-upload --access_key $2 --secret_key $3 $PWD/outputs preafq-hbn 

kubernetes/docker/dockerfile-dmriprep-kube

@@ -0,0 +1,3 @@
+FROM dmriprep:prod
+COPY dmriprep_all.sh /dmriprep_all.sh
+CMD ["/neurodocker/startup.sh", "dmriprep_all.sh"]