Merge pull request #143 from neuroscout/fix_smoothing

FIX: Smoothing in fitlins occurs at incorrect level

Author: adelavega

Dockerfile

@@ -17,6 +17,10 @@ RUN /bin/bash -c "source activate neuro \
       && pip install -q --no-cache-dir -e /src/neuroscout/" \
     && sync
 
+RUN /bin/bash -c "source activate neuro \
+      && pip install -q --no-cache-dir --upgrade git+https://github.com/poldracklab/fitlins.git@maint/0.9.x" \
+    && sync
+
 RUN /bin/bash -c "source activate neuro \
       && pip install -q --no-cache-dir --upgrade -r /src/neuroscout/requirements.txt" \
     && sync

README.md

@@ -49,8 +49,9 @@ Options:
     -w, --work-dir <dir>     Optional Fitlins working directory 
     -c, --n-cpus <n>         Maximum number of threads across all processes
                              [default: 1]
-    -s, --smoothing <k>      Smoothing kernel FWHM at group level
-                             [default: 4]
+    -s, --smoothing <k>      Smoothing to apply in format: FWHM:level:type.
+                             See fitlins documentation for more information.
+                             [default: 4:Dataset:iso]
     -u, --unlock             Unlock datalad dataset
     -n, --neurovault <nv>    Upload mode (disable, all, or group)
                              [default: group]

neuroscout_cli/__init__.py

@@ -1 +1 @@
-__version__ = '0.5.3'
+__version__ = '0.5.4'

neuroscout_cli/cli.py

@@ -14,8 +14,9 @@
     -w, --work-dir <dir>     Optional Fitlins working directory 
     -c, --n-cpus <n>         Maximum number of threads across all processes
                              [default: 1]
-    -s, --smoothing <k>      Smoothing kernel FWHM at group level
-                             [default: 4]
+    -s, --smoothing <k>      Smoothing to apply in format: FWHM:level:type.
+                             See fitlins documentation for more information.
+                             [default: 4:Dataset:iso]
     -u, --unlock             Unlock datalad dataset
     -n, --neurovault <nv>    Upload mode (disable, all, or group)
                              [default: group]
@@ -67,5 +68,9 @@ def main():
                 for bundle in bundles:
                     logging.info("Analysis ID : {}".format(bundle))
                     args['<bundle_id>'] = bundle
-                    command(deepcopy(args)).run()
+                    retcode = command(deepcopy(args)).run()
+                    
+                    # If any execution fails, then exit
+                    if retcode != 0:
+                        sys.exit(retcode)
             sys.exit(0)

neuroscout_cli/commands/run.py

@@ -38,7 +38,7 @@ def run(self, upload_only=False):
                 f'--model={model_path}',
                 '--ignore=/(.*desc-confounds_regressors.*)/',
                 f'--derivatives={str(self.bundle_dir.absolute())} {str(self.preproc_dir.absolute())}',
-                f'--smoothing={self.options["--smoothing"]}:Dataset',
+                f'--smoothing={self.options["--smoothing"]}',
                 f'--estimator={self.options["--estimator"]}',
                 f'--n-cpus={self.options["--n-cpus"]}'
             ]
@@ -72,6 +72,7 @@ def run(self, upload_only=False):
                     "https://github.com/neuroscout/neuroscout-cli/issues\n"
                     "-------------------------------------------------------\n"
                     )
+                return retcode
 
         if neurovault != 'disable':
             model = json.load(open(model_path, 'r'))
@@ -82,6 +83,7 @@ def run(self, upload_only=False):
                 options = json.load((out_dir / 'options.json').open('r'))
                 estimator = options.get('--estimator')
             except:
+                options = None
                 print("No saved options found skipping...")
 
             try:
@@ -118,8 +120,11 @@ def run(self, upload_only=False):
                 fmriprep_version=fmriprep_version,
                 estimator=estimator,
                 cli_version=VERSION,
+                cli_args=options,
                 n_subjects=n_subjects)
 
         # Drop files if no separate install dir, and the user has not said otherwise.
         if not self.install_dir and not no_drop:
-            drop(str(self.preproc_dir.absolute()))
+            drop(str(self.preproc_dir.absolute()))
+        
+        return retcode

requirements.txt

@@ -1,5 +1,5 @@
 docopt==0.6.2
 datalad==0.10.2
 tqdm
-pyns==0.4.7
-git+https://github.com/bids-standard/pybids.git@maint/0.13.x 
+pyns==0.4.8
+git+https://github.com/bids-standard/pybids.git@maint/0.13.x