diff --git a/CHANGES b/CHANGES
index ed2cbb4b8f..8981d0af91 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: Allow control over terminal output for commandline interfaces
 
 Release 0.7.0 (Dec 18, 2012)
 ============================
diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py
index d10c628a7a..17edc222c8 100644
--- a/nipype/interfaces/afni/base.py
+++ b/nipype/interfaces/afni/base.py
@@ -42,7 +42,8 @@ def version():
            Version number as string or None if AFNI not found
 
         """
-        clout = CommandLine(command='afni_vcheck').run()
+        clout = CommandLine(command='afni_vcheck',
+                            terminal_output='allatonce').run()
         out = clout.runtime.stdout
         return out.split('\n')[1]
 
@@ -87,7 +88,8 @@ def standard_image(img_name):
         '''Grab an image from the standard location.
 
         Could be made more fancy to allow for more relocatability'''
-        clout = CommandLine('which afni').run()
+        clout = CommandLine('which afni',
+                            terminal_output='allatonce').run()
         if clout.runtime.returncode is not 0:
             return None
 
diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py
index 04c0412f27..683bec23ed 100644
--- a/nipype/interfaces/base.py
+++ b/nipype/interfaces/base.py
@@ -1024,7 +1024,7 @@ def _read(self, drain):
         self._lastidx = len(self._rows)
 
 
-def run_command(runtime, timeout=0.01):
+def run_command(runtime, output=None, timeout=0.01):
     """
     Run a command, read stdout and stderr, prefix with timestamp. The returned
     runtime contains a merged stdout+stderr log with timestamps
@@ -1038,42 +1038,71 @@ def run_command(runtime, timeout=0.01):
                              shell=True,
                              cwd=runtime.cwd,
                              env=runtime.environ)
-    streams = [
-        Stream('stdout', proc.stdout),
-        Stream('stderr', proc.stderr)
-        ]
+    result = {}
+    if output == 'stream':
+        streams = [
+            Stream('stdout', proc.stdout),
+            Stream('stderr', proc.stderr)
+            ]
 
-    def _process(drain=0):
-        try:
-            res = select.select(streams, [], [], timeout)
-        except select.error, e:
-            iflogger.info(str(e))
-            if e[0] == errno.EINTR:
-                return
+        def _process(drain=0):
+            try:
+                res = select.select(streams, [], [], timeout)
+            except select.error, e:
+                iflogger.info(str(e))
+                if e[0] == errno.EINTR:
+                    return
+                else:
+                    raise
             else:
-                raise
-        else:
-            for stream in res[0]:
-                stream.read(drain)
-
-    while proc.returncode is None:
-        proc.poll()
-        _process()
-    runtime.returncode = proc.returncode
-    _process(drain=1)
-
-    # collect results, merge and return
-    result = {}
-    temp = []
-    for stream in streams:
-        rows = stream._rows
-        temp += rows
-        result[stream._name] = [r[2] for r in rows]
-    temp.sort()
-    result['merged'] = [r[1] for r in temp]
+                for stream in res[0]:
+                    stream.read(drain)
+
+        while proc.returncode is None:
+            proc.poll()
+            _process()
+        _process(drain=1)
+
+        # collect results, merge and return
+        result = {}
+        temp = []
+        for stream in streams:
+            rows = stream._rows
+            temp += rows
+            result[stream._name] = [r[2] for r in rows]
+        temp.sort()
+        result['merged'] = [r[1] for r in temp]
+    if output == 'allatonce':
+        stdout, stderr = proc.communicate()
+        result['stdout'] = stdout.split('\n')
+        result['stderr'] = stderr.split('\n')
+        result['merged'] = ''
+    if output == 'file':
+        errfile = os.path.join(runtime.cwd, 'stderr.nipype')
+        outfile = os.path.join(runtime.cwd, 'stdout.nipype')
+        stderr =  open(errfile, 'wt')
+        stdout =  open(outfile, 'wt')
+        proc = subprocess.Popen(runtime.cmdline,
+                                stdout=stdout,
+                                stderr=stderr,
+                                shell=True,
+                                cwd=runtime.cwd,
+                                env=runtime.environ)
+        ret_code = proc.wait()
+        stderr.flush()
+        stdout.flush()
+        result['stdout'] = [line.strip() for line in open(outfile).readlines()]
+        result['stderr'] = [line.strip() for line in open(errfile).readlines()]
+        result['merged'] = ''
+    if output == 'none':
+        proc.communicate()
+        result['stdout'] = []
+        result['stderr'] = []
+        result['merged'] = ''
     runtime.stderr = '\n'.join(result['stderr'])
     runtime.stdout = '\n'.join(result['stdout'])
     runtime.merged = result['merged']
+    runtime.returncode = proc.returncode
     return runtime
 
 
@@ -1081,7 +1110,9 @@ class CommandLineInputSpec(BaseInterfaceInputSpec):
     args = traits.Str(argstr='%s', desc='Additional parameters to the command')
     environ = traits.DictStrStr(desc='Environment variables', usedefault=True,
                                 nohash=True)
-
+    terminal_output = traits.Enum('stream', 'allatonce', 'file', 'none',
+                                  desc='Control terminal output', nohash=True,
+                                  mandatory=True)
 
 class CommandLine(BaseInterface):
     """Implements functionality to interact with command line programs
@@ -1107,7 +1138,7 @@ class must be instantiated with a command argument
     'ls -al'
 
     >>> cli.inputs.trait_get()
-    {'ignore_exception': False, 'args': '-al', 'environ': {'DISPLAY': ':1'}}
+    {'ignore_exception': False, 'terminal_output': 'stream', 'environ': {'DISPLAY': ':1'}, 'args': '-al'}
 
     >>> cli.inputs.get_hashval()
     ({'args': '-al'}, 'a2f45e04a34630c5f33a75ea2a533cdd')
@@ -1117,6 +1148,7 @@ class must be instantiated with a command argument
     input_spec = CommandLineInputSpec
     _cmd = None
     _version = None
+    _terminal_output = 'stream'
 
     def __init__(self, command=None, **inputs):
         super(CommandLine, self).__init__(**inputs)
@@ -1127,6 +1159,31 @@ def __init__(self, command=None, **inputs):
             raise Exception("Missing command")
         if command:
             self._cmd = command
+        self.inputs.on_trait_change(self._terminal_output_update,
+                                    'terminal_output')
+        if not isdefined(self.inputs.terminal_output):
+            self.inputs.terminal_output = self._terminal_output
+        else:
+            self._terminal_output_update()
+
+    def _terminal_output_update(self):
+        self._terminal_output = self.inputs.terminal_output
+
+    @classmethod
+    def set_default_terminal_output(cls, output_type):
+        """Set the default output type for FSL classes.
+
+        This method is used to set the default output type for all fSL
+        subclasses.  However, setting this will not update the output
+        type for any existing instances.  For these, assign the
+        <instance>.inputs.output_type.
+        """
+
+        if output_type in ['stream', 'allatonce', 'file', 'none']:
+            cls._terminal_output = output_type
+        else:
+            raise AttributeError('Invalid terminal output_type: %s' %
+                                 output_type)
 
     @property
     def cmd(self):
@@ -1207,7 +1264,7 @@ def _run_interface(self, runtime):
         if not self._exists_in_path(self.cmd.split()[0]):
             raise IOError("%s could not be found on host %s" % (self.cmd.split()[0],
                                                                 runtime.hostname))
-        runtime = run_command(runtime)
+        runtime = run_command(runtime, output=self.inputs.terminal_output)
         if runtime.returncode is None or runtime.returncode != 0:
             self.raise_exception(runtime)
 
diff --git a/nipype/interfaces/diffusion_toolkit/base.py b/nipype/interfaces/diffusion_toolkit/base.py
index acb437045a..4e6e6b82ad 100644
--- a/nipype/interfaces/diffusion_toolkit/base.py
+++ b/nipype/interfaces/diffusion_toolkit/base.py
@@ -42,7 +42,8 @@ def version():
            Version number as string or None if FSL not found
 
         """
-        clout = CommandLine(command='dti_recon').run()
+        clout = CommandLine(command='dti_recon',
+                            terminal_output='allatonce').run()
 
         if clout.runtime.returncode is not 0:
             return None
diff --git a/nipype/interfaces/fsl/base.py b/nipype/interfaces/fsl/base.py
index 4f91690af7..19348e017e 100644
--- a/nipype/interfaces/fsl/base.py
+++ b/nipype/interfaces/fsl/base.py
@@ -73,7 +73,8 @@ def version():
         except KeyError:
             return None
         clout = CommandLine(command='cat',
-                            args='%s/etc/fslversion' % (basedir)).run()
+                            args='%s/etc/fslversion' % (basedir),
+                            terminal_output='allatonce').run()
         out = clout.runtime.stdout
         return out.strip('\n')
 
diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py
index 7756e60017..2ac1a2b7a4 100644
--- a/nipype/interfaces/fsl/tests/test_preprocess.py
+++ b/nipype/interfaces/fsl/tests/test_preprocess.py
@@ -219,7 +219,8 @@ def test_flirt():
         # Skip mandatory inputs and the trait methods
         if key in ('trait_added', 'trait_modified', 'in_file', 'reference',
                    'environ', 'output_type', 'out_file', 'out_matrix_file',
-                   'in_matrix_file', 'apply_xfm', 'ignore_exception'):
+                   'in_matrix_file', 'apply_xfm', 'ignore_exception',
+                   'terminal_output'):
             continue
         param = None
         value = None
diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py
index a7c29be34e..f03eaf4a84 100644
--- a/nipype/interfaces/matlab.py
+++ b/nipype/interfaces/matlab.py
@@ -17,7 +17,8 @@ def get_matlab_command():
         matlab_cmd = 'matlab'
 
     try:
-        res = CommandLine(command='which', args=matlab_cmd).run()
+        res = CommandLine(command='which', args=matlab_cmd,
+                          terminal_output='allatonce').run()
         matlab_path = res.runtime.stdout.strip()
     except Exception, e:
         return None
@@ -95,6 +96,9 @@ def __init__(self, matlab_cmd = None, **inputs):
                 not isdefined(self.inputs.uses_mcr):
             if config.getboolean('execution','single_thread_matlab'):
                 self.inputs.single_comp_thread = True
+        # For matlab commands force all output to be returned since matlab
+        # does not have a clean way of notifying an error
+        self.inputs.terminal_output = 'allatonce'
 
     @classmethod
     def set_default_matlab_cmd(cls, matlab_cmd):
@@ -130,6 +134,7 @@ def set_default_paths(cls, paths):
         cls._default_paths = paths
 
     def _run_interface(self,runtime):
+        self.inputs.terminal_output = 'allatonce'
         runtime = super(MatlabCommand, self)._run_interface(runtime)
         try:
             # Matlab can leave the terminal in a barbbled state
diff --git a/nipype/interfaces/tests/test_base.py b/nipype/interfaces/tests/test_base.py
index f4c7a9d327..b36019b18c 100644
--- a/nipype/interfaces/tests/test_base.py
+++ b/nipype/interfaces/tests/test_base.py
@@ -461,3 +461,53 @@ def test_Commandline_environ():
     ci3.inputs.environ = {'DISPLAY' : ':2'}
     res = ci3.run()
     yield assert_equal, res.runtime.environ['DISPLAY'], ':2'
+
+def test_CommandLine_output():
+    tmp_infile = setup_file()
+    tmpd, name = os.path.split(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+    yield assert_true, os.path.exists(tmp_infile)
+    ci = nib.CommandLine(command='ls -l')
+    ci.inputs.terminal_output = 'allatonce'
+    res = ci.run()
+    yield assert_equal, res.runtime.merged, ''
+    yield assert_true, name in res.runtime.stdout
+    ci = nib.CommandLine(command='ls -l')
+    ci.inputs.terminal_output = 'file'
+    res = ci.run()
+    yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    ci = nib.CommandLine(command='ls -l')
+    ci.inputs.terminal_output = 'none'
+    res = ci.run()
+    yield assert_equal, res.runtime.stdout, ''
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    os.chdir(pwd)
+    teardown_file(tmpd)
+
+def test_global_CommandLine_output():
+    tmp_infile = setup_file()
+    tmpd, name = os.path.split(tmp_infile)
+    pwd = os.getcwd()
+    os.chdir(tmpd)
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_true, name in res.runtime.stdout
+    yield assert_true, os.path.exists(tmp_infile)
+    nib.CommandLine.set_default_terminal_output('allatonce')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_equal, res.runtime.merged, ''
+    yield assert_true, name in res.runtime.stdout
+    nib.CommandLine.set_default_terminal_output('file')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    nib.CommandLine.set_default_terminal_output('none')
+    ci = nib.CommandLine(command='ls -l')
+    res = ci.run()
+    yield assert_equal, res.runtime.stdout, ''
+    os.chdir(pwd)
+    teardown_file(tmpd)
\ No newline at end of file
diff --git a/nipype/pipeline/plugins/condor.py b/nipype/pipeline/plugins/condor.py
index d585be76b0..00db00ef74 100644
--- a/nipype/pipeline/plugins/condor.py
+++ b/nipype/pipeline/plugins/condor.py
@@ -45,7 +45,8 @@ def __init__(self, **kwargs):
         super(CondorPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        cmd = CommandLine('condor_q')
+        cmd = CommandLine('condor_q',
+                          terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check condor cluster
         oldlevel = iflogger.level
@@ -57,7 +58,8 @@ def _is_pending(self, taskid):
         return False
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('condor_qsub', environ=os.environ.data)
+        cmd = CommandLine('condor_qsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:
diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py
index 0ee20acf4c..2d2faaae19 100644
--- a/nipype/pipeline/plugins/dagman.py
+++ b/nipype/pipeline/plugins/dagman.py
@@ -95,7 +95,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                                      % (' '.join([str(i) for i in parents]),
                                         child))
         # hand over DAG to condor_dagman
-        cmd = CommandLine('condor_submit_dag', environ=os.environ.data)
+        cmd = CommandLine('condor_submit_dag', environ=os.environ.data,
+                          terminal_output='allatonce')
         # needs -update_submit or re-running a workflow will fail
         cmd.inputs.args = '-update_submit %s %s' % (dagfilename,
                                                     self._dagman_args)
diff --git a/nipype/pipeline/plugins/lsf.py b/nipype/pipeline/plugins/lsf.py
index 632164ee32..6f9b1bb3d8 100644
--- a/nipype/pipeline/plugins/lsf.py
+++ b/nipype/pipeline/plugins/lsf.py
@@ -43,7 +43,8 @@ def _is_pending(self, taskid):
         and 'RUN' when it is actively being processed. But _is_pending should return True until a job has
         finished and is ready to be checked for completeness. So return True if status is either 'PEND'
         or 'RUN'"""
-        cmd = CommandLine('bjobs')
+        cmd = CommandLine('bjobs',
+                          terminal_output='allatonce')
         cmd.inputs.args = '%d' % taskid
         # check lsf task
         oldlevel = iflogger.level
@@ -57,7 +58,8 @@ def _is_pending(self, taskid):
             return False
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('bsub', environ=os.environ.data)
+        cmd = CommandLine('bsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         bsubargs = ''
         if self._bsub_args:
diff --git a/nipype/pipeline/plugins/pbs.py b/nipype/pipeline/plugins/pbs.py
index f8a177dc69..d1b9aff43d 100644
--- a/nipype/pipeline/plugins/pbs.py
+++ b/nipype/pipeline/plugins/pbs.py
@@ -45,7 +45,8 @@ def _is_pending(self, taskid):
         return  errmsg not in e
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('qsub', environ=os.environ.data)
+        cmd = CommandLine('qsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:
diff --git a/nipype/pipeline/plugins/pbsgraph.py b/nipype/pipeline/plugins/pbsgraph.py
index 710f93a8a1..d48d305a5e 100644
--- a/nipype/pipeline/plugins/pbsgraph.py
+++ b/nipype/pipeline/plugins/pbsgraph.py
@@ -53,7 +53,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                 fp.writelines('job%05d=`qsub %s %s %s`\n' % (idx, deps,
                                                              qsub_args,
                                                              batchscriptfile))
-        cmd = CommandLine('sh', environ=os.environ.data)
+        cmd = CommandLine('sh', environ=os.environ.data,
+                          terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')
diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py
index 6cc95e4d11..d9f3d2519f 100644
--- a/nipype/pipeline/plugins/sge.py
+++ b/nipype/pipeline/plugins/sge.py
@@ -59,7 +59,8 @@ def _is_pending(self, taskid):
         return o.startswith('=')
 
     def _submit_batchtask(self, scriptfile, node):
-        cmd = CommandLine('qsub', environ=os.environ.data)
+        cmd = CommandLine('qsub', environ=os.environ.data,
+                          terminal_output='allatonce')
         path = os.path.dirname(scriptfile)
         qsubargs = ''
         if self._qsub_args:
diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py
index 11ac4e4477..066ecb587f 100644
--- a/nipype/pipeline/plugins/sgegraph.py
+++ b/nipype/pipeline/plugins/sgegraph.py
@@ -88,7 +88,8 @@ def _submit_graph(self, pyfiles, dependencies, nodes):
                     batchscript=batchscriptfile)
                 fp.writelines(full_line)
 
-        cmd = CommandLine('bash', environ=os.environ.data)
+        cmd = CommandLine('bash', environ=os.environ.data,
+                          terminal_output='allatonce')
         cmd.inputs.args = '%s' % submitjobsfile
         cmd.run()
         logger.info('submitted all jobs to queue')
diff --git a/nipype/pipeline/utils.py b/nipype/pipeline/utils.py
index 48f7bf3acb..1d263bcc7e 100644
--- a/nipype/pipeline/utils.py
+++ b/nipype/pipeline/utils.py
@@ -570,7 +570,7 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
     logger.info('Creating detailed dot file: %s' % outfname)
     _write_detailed_dot(graph, outfname)
     cmd = 'dot -T%s -O %s' % (format, outfname)
-    res = CommandLine(cmd).run()
+    res = CommandLine(cmd, terminal_output='allatonce').run()
     if res.runtime.returncode:
         logger.warn('dot2png: %s', res.runtime.stderr)
     pklgraph = _create_dot_graph(graph, show_connectinfo, simple_form)
@@ -581,7 +581,7 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
     nx.write_dot(pklgraph, outfname)
     logger.info('Creating dot file: %s' % outfname)
     cmd = 'dot -T%s -O %s' % (format, outfname)
-    res = CommandLine(cmd).run()
+    res = CommandLine(cmd, terminal_output='allatonce').run()
     if res.runtime.returncode:
         logger.warn('dot2png: %s', res.runtime.stderr)
     if show:
diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py
index 875b1b5ee6..a380a8932d 100644
--- a/nipype/utils/docparse.py
+++ b/nipype/utils/docparse.py
@@ -247,7 +247,8 @@ def get_doc(cmd, opt_map, help_flag=None, trap_error=True):
         The formated docstring
 
     """
-    res = CommandLine('which %s' % cmd.split(' ')[0]).run()
+    res = CommandLine('which %s' % cmd.split(' ')[0],
+                      terminal_output='allatonce').run()
     cmd_path = res.runtime.stdout.strip()
     if cmd_path == '':
         raise Exception('Command %s not found'%cmd.split(' ')[0])
@@ -320,7 +321,8 @@ def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True):
         Contains a mapping from input to command line variables
 
     """
-    res = CommandLine('which %s' % cmd.split(' ')[0]).run()
+    res = CommandLine('which %s' % cmd.split(' ')[0],
+                      terminal_output='allatonce').run()
     cmd_path = res.runtime.stdout.strip()
     if cmd_path == '':
         raise Exception('Command %s not found'%cmd.split(' ')[0])