Corrects output for slurm outfiles.

Environment variables can override this, but we are now storing the
slurm.out files in the batch directory with the other batchfiles.
This commit also removes the hardcoded link to the bbr file in 
$FSLDIR/etc/ and replaces it with a relative path starting from 
$FSLDIR.

Author: Chad Cumba

nipype/pipeline/plugins/slurm.py

@@ -35,8 +35,8 @@ class SLURMPlugin(SGELikeBatchManagerBase):
 
     def __init__(self, **kwargs):
 
-        template="""#!/bin/sh
-        """
+        template="#!/bin/bash"
+        
         self._retry_timeout = 2
         self._max_tries = 2
         self._template = template
@@ -84,9 +84,9 @@ def _submit_batchtask(self, scriptfile, node):
             else:
                 sbatch_args += (" " + node.plugin_args['sbatch_args'])
         if '-o' not in sbatch_args:
-            sbatch_args = '%s -o %s' % (sbatch_args, path)
+            sbatch_args = '%s -o %s' % (sbatch_args, os.path.join(path, 'slurm-%j.out'))
         if '-e' not in sbatch_args:
-            sbatch_args = '%s -e %s' % (sbatch_args, path)
+            sbatch_args = '%s -e %s' % (sbatch_args, os.path.join(path, 'slurm-%j.out'))
         if '-p' not in sbatch_args:
             sbatch_args = '%s -p normal' % (sbatch_args)
         if '-n' not in sbatch_args:
@@ -123,6 +123,7 @@ def _submit_batchtask(self, scriptfile, node):
                                                   str(e))))
             else:
                 break
+        logger.debug('Ran command ({0})'.format(cmd.cmdline))
         iflogger.setLevel(oldlevel)
         # retrieve taskid
         lines = [line for line in result.runtime.stdout.split('\n') if line]

nipype/workflows/fmri/fsl/preprocess.py

@@ -6,6 +6,7 @@
 import nipype.pipeline.engine as pe          # pypeline engine
 import nipype.interfaces.freesurfer as fs    # freesurfer
 import nipype.interfaces.spm as spm
+import os
 
 from ...smri.freesurfer.utils import create_getmask_flow
 
@@ -1156,7 +1157,8 @@ def create_reg_workflow(name='registration'):
     mean2anatbbr = pe.Node(fsl.FLIRT(), name='mean2anatbbr')
     mean2anatbbr.inputs.dof = 6
     mean2anatbbr.inputs.cost = 'bbr'
-    mean2anatbbr.inputs.schedule = '/usr/local/fsl/etc/flirtsch/bbr.sch'
+    os.environ['FSLDIR']
+    mean2anatbbr.inputs.schedule = os.path.join(os.environ['FSLDIR'],'etc/flirtsch/bbr.sch')
     register.connect(inputnode, 'mean_image', mean2anatbbr, 'in_file')
     register.connect(binarize, 'out_file', mean2anatbbr, 'wm_seg')
     register.connect(inputnode, 'anatomical_image', mean2anatbbr, 'reference')