Merge pull request #787 from oesteban/enh/NewFreeSurfer

[ENH] New FreeSurfer's license mechanism

.circle/tests.sh

@@ -55,7 +55,15 @@ case ${CIRCLE_NODE_INDEX} in
     rm -r $HOME/ds054/out/fmriprep/sub-100185/log
     ;;
   1)
+    # Do not use --fs-license-file to exercise using the env variable
     fmriprep-docker -i poldracklab/fmriprep:latest --config $HOME/nipype.cfg -w $HOME/ds005/scratch $HOME/data/ds005 $HOME/ds005/out participant --debug --write-graph --use-syn-sdc --use-aroma --ignore-aroma-denoising-errors
     find ~/ds005/scratch -not -name "*.svg" -not -name "*.html" -not -name "*.rst" -not -name "*.mat" -not -name "*.lta" -type f -delete
+    # Check for --fs-license-file not defined
+    set +e
+    unset FS_LICENSE
+    fmriprep-docker -i poldracklab/fmriprep:latest --config $HOME/nipype.cfg -w $HOME/ds005/scratch $HOME/data/ds005 $HOME/ds005/out participant --debug --write-graph --use-syn-sdc --use-aroma --ignore-aroma-denoising-errors
+    RET=$?
+    set -e
+    [[ "$RET" -eq "1" ]]
     ;;
 esac

CHANGES.rst

@@ -1,6 +1,8 @@
 Next release
 ============
 
+* [FIX] Adopt new FreeSurfer license mechanism (#787)
+
 
 1.0.0-rc9 (2nd of November 2017)
 ================================

Dockerfile

@@ -22,7 +22,7 @@ RUN apt-get update && \
     apt-get update
 
 # Installing freesurfer
-RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz | tar zxv -C /opt \
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
     --exclude='freesurfer/trctrain' \
     --exclude='freesurfer/subjects/fsaverage_sym' \
     --exclude='freesurfer/subjects/fsaverage3' \
@@ -53,7 +53,6 @@ ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
 ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
     MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
     PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
-RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
 
 # Installing Neurodebian packages (FSL, AFNI, git)
 RUN apt-get update && \

circle.yml

@@ -8,6 +8,7 @@ machine:
     DS005_URL: "${OSF_PROJECT}/57f32a429ad5a101f977eb75"
     DS005_FS_URL: "${OSF_PROJECT}/58fe59eb594d900250960180"
     DS054_URL: "${OSF_PROJECT}/57f32c22594d9001ef91bf9e"
+    FS_LICENSE: /tmp/fslicense/license.txt
   services:
     - docker
 
@@ -20,6 +21,7 @@ dependencies:
     - mkdir -p $HOME/ds005/out && sudo setfacl -R -d -m group:ubuntu:rwx $HOME/ds005 && sudo setfacl -R -m group:ubuntu:rwx $HOME/ds005
     - mkdir -p $HOME/ds054 && sudo setfacl -d -m group:ubuntu:rwx $HOME/ds054 && sudo setfacl -m group:ubuntu:rwx $HOME/ds054
     - mkdir -p $HOME/docs && sudo setfacl -d -m group:ubuntu:rwx $HOME/docs && sudo setfacl -m group:ubuntu:rwx $HOME/docs
+    - mkdir -p /tmp/fslicense && cd /tmp/fslicense && echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh
     # Download test data
     - if [[ ! -d $HOME/data/ds005 ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O ds005_downsampled.tar.gz "${DS005_URL}" && tar xzf ds005_downsampled.tar.gz -C $HOME/data/; fi
     - if [[ ! -d $HOME/data/ds054 ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O ds054_downsampled.tar.gz "${DS054_URL}" && tar xzf ds054_downsampled.tar.gz -C $HOME/data/; fi

docs/installation.rst

@@ -37,7 +37,7 @@ print it out for reporting purposes, and then run the command, e.g.::
     $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
     RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
         -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
-        /data /out participant
+        /data /out participant --no-freesurfer
     ...
 
 You may also invoke ``docker`` directly::
@@ -47,7 +47,7 @@ You may also invoke ``docker`` directly::
         -v filepath/to/output/dir:/out \
         poldracklab/fmriprep:latest \
         /data /out/out \
-        participant
+        participant --no-freesurfer
 
 For example: ::
 
@@ -57,11 +57,50 @@ For example: ::
         poldracklab/fmriprep:latest \
         /data /out/out \
         participant \
-        --ignore fieldmaps
+        --ignore fieldmaps --no-freesurfer
 
 See `External Dependencies`_ for more information (e.g., specific versions) on
 what is included in the latest Docker images.
 
+If the flag ``--no-freesurfer`` is not set, then FreeSurfer will require a proper
+license file.
+It is possible to run the docker container pointing the image to a local path
+where a valid license file is stored.
+For example, if the license is stored in the ``$HOME/.licenses/freesurfer/license.txt``
+file on the host system: ::
+
+    $ docker run -ti --rm \
+        -v $HOME/fullds005:/data:ro \
+        -v $HOME/dockerout:/out \
+        -v $HOME/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
+        poldracklab/fmriprep:latest \
+        /data /out/out \
+        participant \
+        --ignore fieldmaps
+
+It is also possible to run ``fmriprep-docker`` with FreeSurfer processing: ::
+
+    $ fmriprep-docker --fs-license-file $HOME/.licenses/freesurfer/license.txt \
+        /path/to/data/dir /path/to/output/dir participant
+    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
+        -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
+        -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
+        /data /out participant
+    ...
+
+If the environment variable ``$FS_LICENSE`` is set in the host system, then
+it will automatically used by ``fmriprep-docker``. For instance, the following
+would be equivalent to the latest example: ::
+
+    $ export FS_LICENSE=$HOME/.licenses/freesurfer/license.txt
+    $ fmriprep-docker /path/to/data/dir /path/to/output/dir participant
+    RUNNING: docker run --rm -it -v /path/to/data/dir:/data:ro \
+        -v /home/user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt \
+        -v /path/to_output/dir:/out poldracklab/fmriprep:1.0.0 \
+        /data /out participant
+    ...
+
+
 Singularity Container
 =====================
 

fmriprep/cli/run.py

@@ -169,6 +169,10 @@ def get_parser():
                       help='disable FreeSurfer preprocessing')
     g_fs.add_argument('--no-submm-recon', action='store_false', dest='hires',
                       help='disable sub-millimeter (hires) reconstruction')
+    g_fs.add_argument(
+        '--fs-license-file', metavar='PATH', type=os.path.abspath,
+        help='Path to FreeSurfer license key file. Get it (for free) by registering'
+             ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
 
     g_other = parser.add_argument_group('Other options')
     g_other.add_argument('-w', '--work-dir', action='store', default='work',
@@ -194,6 +198,16 @@ def main():
     if opts.debug:
         logger.setLevel(logging.DEBUG)
 
+    default_license = op.join(os.getenv('FREESURFER_HOME', ''), 'license.txt')
+    # Precedence: --fs-license-file, $FS_LICENSE, default_license
+    license_file = opts.fs_license_file or os.getenv('FS_LICENSE', default_license)
+    if opts.freesurfer:
+        if not os.path.exists(license_file):
+            raise RuntimeError('ERROR: when --no-freesurfer is not set, a valid '
+                               'license file is required for FreeSurfer to run.')
+        else:
+            os.environ['FS_LICENSE'] = license_file
+
     # Validity of some inputs - OE should be done in parse_args?
     # ERROR check if use_aroma was specified, but the correct template was not
     if opts.use_aroma and (opts.template != 'MNI152NLin2009cAsym' or

wrapper/fmriprep_docker.py

@@ -5,7 +5,6 @@
 import sys
 import os
 import re
-import argparse
 import subprocess
 
 standard_library.install_aliases()
@@ -154,7 +153,8 @@ def merge_help(wrapper_help, target_help):
 
     # Make sure we're not clobbering options we don't mean to
     overlap = set(w_flags).intersection(t_flags)
-    expected_overlap = set(['h', 'v', 'w', 'output-grid-reference'])
+    expected_overlap = set(['h', 'v', 'w', 'output-grid-reference',
+                            'fs-license-file'])
     assert overlap == expected_overlap, "Clobbering options: {}".format(
         ', '.join(overlap - expected_overlap))
 
@@ -194,11 +194,13 @@ def merge_help(wrapper_help, target_help):
     sections.append(w_groups[2])
 
     # All remaining sections, show target then wrapper (skipping duplicates)
-    sections.extend(t_groups[3:] + w_groups[5:])
+    sections.extend(t_groups[3:] + w_groups[6:])
     return '\n\n'.join(sections)
 
 
-def main():
+def get_parser():
+    """Defines the command line interface of the wrapper"""
+    import argparse
     parser = argparse.ArgumentParser(
         description='fMRI Preprocessing workflow',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -231,6 +233,11 @@ def main():
                         type=os.path.abspath,
                         help='Grid reference image for resampling BOLD files to volume template '
                              'space.')
+    g_wrap.add_argument(
+        '--fs-license-file', metavar='PATH', type=os.path.abspath,
+        default=os.getenv('FS_LICENSE', None),
+        help='Path to FreeSurfer license key file. Get it (for free) by registering'
+             ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
 
     # Developer patch/shell options
     g_dev = parser.add_argument_group(
@@ -250,6 +257,13 @@ def main():
     g_dev.add_argument('--config', metavar='PATH', action='store',
                        type=os.path.abspath, help='Use custom nipype.cfg file')
 
+    return parser
+
+
+def main():
+    """Entry point"""
+
+    parser = get_parser()
     # Capture additional arguments to pass inside container
     opts, unknown_args = parser.parse_known_args()
 
@@ -315,6 +329,11 @@ def main():
         if repo_path is not None:
             command.extend(['-v', '{}:{}:ro'.format(repo_path, pkg_path)])
 
+    if opts.fs_license_file:
+        command.extend([
+            '-v', '{}:/opt/freesurfer/license.txt:ro'.format(
+                opts.fs_license_file)])
+
     main_args = []
     if opts.bids_dir:
         command.extend(['-v', ':'.join((opts.bids_dir, '/data', 'ro'))])