enh: install datalad/dcm2niix on circle build

Author: mgxd

docker/generate_dockerfiles.sh

@@ -68,10 +68,11 @@ function generate_base_dockerfile() {
     --spm12 version=r7219 \
     --env 'LD_LIBRARY_PATH=/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH' \
     --freesurfer version=6.0.0-min \
+    --dcm2niix version=v1.0.20190902 \
     --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tCjUxNzIKICpDdnVtdkVWM3pUZmcKRlM1Si8yYzFhZ2c0RQoiID4gL29wdC9mcmVlc3VyZmVyLTYuMC4wLW1pbi9saWNlbnNlLnR4dA==" | base64 -d | sh' \
     --install afni ants apt-utils bzip2 convert3d file fsl-core \
               fsl-mni152-templates fusefat g++ git graphviz make python ruby \
-              unzip xvfb \
+              unzip xvfb git-annex-standalone \
     --add-to-entrypoint "source /etc/fsl/fsl.sh && source /etc/afni/afni.sh" \
     --env ANTSPATH='/usr/lib/ants' \
           PATH='/usr/lib/ants:$PATH' \

nipype/info.py

@@ -182,6 +182,7 @@ def get_nipype_gitversion():
 ]
 
 EXTRA_REQUIRES = {
+    'data': ['datalad'],
     'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'],
     'duecredit': ['duecredit'],
     'nipy': ['nitime', 'nilearn<0.5.0', 'dipy', 'nipy', 'matplotlib'],

nipype/interfaces/dcm2nii.py

@@ -425,7 +425,7 @@ def _parse_stdout(self, stdout):
         filenames = []
         for line in stdout.split("\n"):
             if line.startswith("Convert "):  # output
-                fname = str(re.search('\S+/\S+', line).group(0))
+                fname = str(re.search(r'\S+/\S+', line).group(0))
                 filenames.append(os.path.abspath(fname))
         return filenames