diff --git a/.gitignore b/.gitignore
index d6996550dc..df018f0ead 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,6 +16,7 @@
 .project
 .pydevproject
 *.py.orig
+.DS_Store
 
 # Not sure what the next one is for
 *.kpf
diff --git a/bin/nib-dicomfs b/bin/nib-dicomfs
index 115fd4e486..05b6a50afc 100755
--- a/bin/nib-dicomfs
+++ b/bin/nib-dicomfs
@@ -9,213 +9,7 @@
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 # Copyright (C) 2011 Christian Haselgrove
 
-import sys
-import os
-import stat
-import errno
-import time
-import locale
-import logging
-import fuse
-import nibabel as nib
-import nibabel.dft as dft
-
-from optparse import OptionParser, Option
-
-uid = os.getuid()
-gid = os.getgid()
-encoding = locale.getdefaultlocale()[1]
-
-fuse.fuse_python_api = (0, 2)
-
-logger = logging.getLogger('nibabel.dft')
-
-class FileHandle:
-
-    def __init__(self, fno):
-        self.fno = fno
-        self.keep_cache = False
-        self.direct_io = False
-        return
-
-    def __str__(self):
-        return 'FileHandle(%d)' % self.fno
-
-class DICOMFS(fuse.Fuse):
-
-    def __init__(self, *args, **kwargs):
-        self.followlinks = kwargs.pop('followlinks', False)
-        fuse.Fuse.__init__(self, *args, **kwargs)
-        self.fhs = {}
-        return
-
-    def get_paths(self):
-        paths = {}
-        for study in dft.get_studies(self.dicom_path, self.followlinks):
-            pd = paths.setdefault(study.patient_name_or_uid(), {})
-            patient_info = 'patient information\n'
-            patient_info = 'name: %s\n' % study.patient_name
-            patient_info += 'ID: %s\n' % study.patient_id
-            patient_info += 'birth date: %s\n' % study.patient_birth_date
-            patient_info += 'sex: %s\n' % study.patient_sex
-            pd['INFO'] = patient_info.encode('ascii', 'replace')
-            study_datetime = '%s_%s' % (study.date, study.time)
-            study_info = 'study info\n'
-            study_info += 'UID: %s\n' % study.uid
-            study_info += 'date: %s\n' % study.date
-            study_info += 'time: %s\n' % study.time
-            study_info += 'comments: %s\n' % study.comments
-            d = {'INFO': study_info.encode('ascii', 'replace')}
-            for series in study.series:
-                series_info = 'series info\n'
-                series_info += 'UID: %s\n' % series.uid
-                series_info += 'number: %s\n' % series.number
-                series_info += 'description: %s\n' % series.description
-                series_info += 'rows: %d\n' % series.rows
-                series_info += 'columns: %d\n' % series.columns
-                series_info += 'bits allocated: %d\n' % series.bits_allocated
-                series_info += 'bits stored: %d\n' % series.bits_stored
-                series_info += 'storage instances: %d\n' % len(series.storage_instances)
-                d[series.number] = {'INFO': series_info.encode('ascii', 'replace'),
-                                    '%s.nii' % series.number: (series.nifti_size, series.as_nifti),
-                                    '%s.png' % series.number: (series.png_size, series.as_png)}
-            pd[study_datetime] = d
-        return paths
-
-    def match_path(self, path):
-        wd = self.get_paths()
-        if path == '/':
-            logger.debug('return root')
-            return wd
-        for part in path.lstrip('/').split('/'):
-            logger.debug("path:%s part:%s" % (path, part))
-            if part not in wd:
-                return None
-            wd = wd[part]
-        logger.debug('return')
-        return wd
-
-    def readdir(self, path, fh):
-        logger.info('readdir %s' % (path,))
-        matched_path = self.match_path(path)
-        if matched_path is None:
-            return -errno.ENOENT
-        logger.debug('matched %s' % (matched_path,))
-        fnames = [ k.encode('ascii', 'replace') for k in matched_path.keys() ]
-        fnames.append('.')
-        fnames.append('..')
-        return [ fuse.Direntry(f) for f in fnames ]
-
-    def getattr(self, path):
-        logger.debug('getattr %s' % path)
-        matched_path = self.match_path(path)
-        logger.debug('matched: %s' % (matched_path,))
-        now = time.time()
-        st = fuse.Stat()
-        if isinstance(matched_path, dict):
-            st.st_mode = stat.S_IFDIR | 0755
-            st.st_ctime = now
-            st.st_mtime = now
-            st.st_atime = now
-            st.st_uid = uid
-            st.st_gid = gid
-            st.st_nlink = len(matched_path)
-            return st
-        if isinstance(matched_path, str):
-            st.st_mode = stat.S_IFREG | 0644
-            st.st_ctime = now
-            st.st_mtime = now
-            st.st_atime = now
-            st.st_uid = uid
-            st.st_gid = gid
-            st.st_size = len(matched_path)
-            st.st_nlink = 1
-            return st
-        if isinstance(matched_path, tuple):
-            st.st_mode = stat.S_IFREG | 0644
-            st.st_ctime = now
-            st.st_mtime = now
-            st.st_atime = now
-            st.st_uid = uid
-            st.st_gid = gid
-            st.st_size = matched_path[0]()
-            st.st_nlink = 1
-            return st
-        return -errno.ENOENT
-
-    def open(self, path, flags):
-        logger.debug('open %s' % (path,))
-        matched_path = self.match_path(path)
-        if matched_path is None:
-            return -errno.ENOENT
-        for i in range(1, 10):
-            if i not in self.fhs:
-                if isinstance(matched_path, str):
-                    self.fhs[i] = matched_path
-                elif isinstance(matched_path, tuple):
-                    self.fhs[i] = matched_path[1]()
-                else:
-                    raise -errno.EFTYPE
-                return FileHandle(i)
-        raise -errno.ENFILE
-
-    # not done
-    def read(self, path, size, offset, fh):
-        logger.debug('read')
-        logger.debug(path)
-        logger.debug(size)
-        logger.debug(offset)
-        logger.debug(fh)
-        return self.fhs[fh.fno][offset:offset+size]
-
-    def release(self, path, flags, fh):
-        logger.debug('release')
-        logger.debug(path)
-        logger.debug(fh)
-        del self.fhs[fh.fno]
-        return
-
-def get_opt_parser():
-    # use module docstring for help output
-    p = OptionParser(
-                usage="%s [OPTIONS] <DIRECTORY CONTAINING DICOMSs> <mount point>"
-                      % os.path.basename(sys.argv[0]),
-                version="%prog " + nib.__version__)
-
-    p.add_options([
-        Option("-v", "--verbose", action="count",
-               dest="verbose", default=0,
-               help="make noise.  Could be specified multiple times"),
-        ])
-
-    p.add_options([
-        Option("-L", "--follow-links", action="store_true",
-               dest="followlinks", default=False,
-               help="Follow symbolic links in DICOM directory"),
-        ])
-    return p
+from nibabel.cmdline.dicomfs import main
 
 if __name__ == '__main__':
-    parser = get_opt_parser()
-    (opts, files) = parser.parse_args()
-
-    if opts.verbose:
-        logger.addHandler(logging.StreamHandler(sys.stdout))
-        logger.setLevel(opts.verbose > 1 and logging.DEBUG or logging.INFO)
-
-    if len(files) != 2:
-        sys.stderr.write("Please provide two arguments:\n%s\n"  % parser.usage)
-        sys.exit(1)
-
-    fs = DICOMFS(dash_s_do='setsingle', followlinks=opts.followlinks)
-    fs.parse(['-f', '-s', files[1]])
-    fs.dicom_path = files[0].decode(encoding)
-    try:
-        fs.main()
-    except fuse.FuseError:
-        # fuse prints the error message
-        sys.exit(1)
-
-    sys.exit(0)
-
-# eof
+    main()
\ No newline at end of file
diff --git a/bin/nib-nifti-dx b/bin/nib-nifti-dx
index 40122acd16..d317585286 100755
--- a/bin/nib-nifti-dx
+++ b/bin/nib-nifti-dx
@@ -8,32 +8,8 @@
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 ''' Print nifti diagnostics for header files '''
-from __future__ import division, print_function, absolute_import
-
-import sys
-
-from optparse import OptionParser
-
-import nibabel as nib
-
-
-def main():
-    """ Go go team """
-    parser = OptionParser(
-        usage="%s [FILE ...]\n\n" % sys.argv[0] + __doc__,
-        version="%prog " + nib.__version__)
-    (opts, files) = parser.parse_args()
-
-    for fname in files:
-        with nib.openers.ImageOpener(fname) as fobj:
-            hdr = fobj.read(nib.nifti1.header_dtype.itemsize)
-        result = nib.Nifti1Header.diagnose_binaryblock(hdr)
-        if len(result):
-            print('Picky header check output for "%s"\n' % fname)
-            print(result + '\n')
-        else:
-            print('Header for "%s" is clean' % fname)
 
+from nibabel.cmdline.nifti_dx import main
 
 if __name__ == '__main__':
     main()
diff --git a/bin/parrec2nii b/bin/parrec2nii
index 4856af9986..27a1abca05 100755
--- a/bin/parrec2nii
+++ b/bin/parrec2nii
@@ -2,7 +2,7 @@
 """PAR/REC to NIfTI converter
 """
 
-from nibabel.parrec2nii_cmd import main
+from nibabel.cmdline.parrec2nii import main
 
 
 if __name__ == '__main__':
diff --git a/nibabel/cmdline/dicomfs.py b/nibabel/cmdline/dicomfs.py
new file mode 100644
index 0000000000..c54c07f966
--- /dev/null
+++ b/nibabel/cmdline/dicomfs.py
@@ -0,0 +1,241 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+# Copyright (C) 2011 Christian Haselgrove
+
+import sys
+import os
+import stat
+import errno
+import time
+import locale
+import logging
+
+
+class dummy_fuse(object):
+    """Dummy fuse "module" so that nose does not blow during doctests"""
+    Fuse = object
+
+
+try:
+    import fuse
+    uid = os.getuid()
+    gid = os.getgid()
+except ImportError:
+    fuse = dummy_fuse
+
+import nibabel as nib
+import nibabel.dft as dft
+
+from optparse import OptionParser, Option
+
+encoding = locale.getdefaultlocale()[1]
+
+fuse.fuse_python_api = (0, 2)
+
+logger = logging.getLogger('nibabel.dft')
+
+
+class FileHandle:
+
+    def __init__(self, fno):
+        self.fno = fno
+        self.keep_cache = False
+        self.direct_io = False
+        return
+
+    def __str__(self):
+        return 'FileHandle(%d)' % self.fno
+
+
+class DICOMFS(fuse.Fuse):
+
+    def __init__(self, *args, **kwargs):
+        if fuse is dummy_fuse:
+            raise RuntimeError(
+                "fuse module is not available, install it to use DICOMFS")
+        self.followlinks = kwargs.pop('followlinks', False)
+        self.dicom_path = kwargs.pop('dicom_path', None)
+        fuse.Fuse.__init__(self, *args, **kwargs)
+        self.fhs = {}
+        return
+
+    def get_paths(self):
+        paths = {}
+        for study in dft.get_studies(self.dicom_path, self.followlinks):
+            pd = paths.setdefault(study.patient_name_or_uid(), {})
+            patient_info = 'patient information\n'
+            patient_info = 'name: %s\n' % study.patient_name
+            patient_info += 'ID: %s\n' % study.patient_id
+            patient_info += 'birth date: %s\n' % study.patient_birth_date
+            patient_info += 'sex: %s\n' % study.patient_sex
+            pd['INFO'] = patient_info.encode('ascii', 'replace')
+            study_datetime = '%s_%s' % (study.date, study.time)
+            study_info = 'study info\n'
+            study_info += 'UID: %s\n' % study.uid
+            study_info += 'date: %s\n' % study.date
+            study_info += 'time: %s\n' % study.time
+            study_info += 'comments: %s\n' % study.comments
+            d = {'INFO': study_info.encode('ascii', 'replace')}
+            for series in study.series:
+                series_info = 'series info\n'
+                series_info += 'UID: %s\n' % series.uid
+                series_info += 'number: %s\n' % series.number
+                series_info += 'description: %s\n' % series.description
+                series_info += 'rows: %d\n' % series.rows
+                series_info += 'columns: %d\n' % series.columns
+                series_info += 'bits allocated: %d\n' % series.bits_allocated
+                series_info += 'bits stored: %d\n' % series.bits_stored
+                series_info += 'storage instances: %d\n' % len(series.storage_instances)
+                d[series.number] = {'INFO': series_info.encode('ascii', 'replace'),
+                                    '%s.nii' % series.number: (series.nifti_size, series.as_nifti),
+                                    '%s.png' % series.number: (series.png_size, series.as_png)}
+            pd[study_datetime] = d
+        return paths
+
+    def match_path(self, path):
+        wd = self.get_paths()
+        if path == '/':
+            logger.debug('return root')
+            return wd
+        for part in path.lstrip('/').split('/'):
+            logger.debug("path:%s part:%s" % (path, part))
+            if part not in wd:
+                return None
+            wd = wd[part]
+        logger.debug('return')
+        return wd
+
+    def readdir(self, path, fh):
+        logger.info('readdir %s' % (path,))
+        matched_path = self.match_path(path)
+        if matched_path is None:
+            return -errno.ENOENT
+        logger.debug('matched %s' % (matched_path,))
+        fnames = [k.encode('ascii', 'replace') for k in matched_path.keys()]
+        fnames.append('.')
+        fnames.append('..')
+        return [fuse.Direntry(f) for f in fnames]
+
+    def getattr(self, path):
+        logger.debug('getattr %s' % path)
+        matched_path = self.match_path(path)
+        logger.debug('matched: %s' % (matched_path,))
+        now = time.time()
+        st = fuse.Stat()
+        if isinstance(matched_path, dict):
+            st.st_mode = stat.S_IFDIR | 0o755
+            st.st_ctime = now
+            st.st_mtime = now
+            st.st_atime = now
+            st.st_uid = uid
+            st.st_gid = gid
+            st.st_nlink = len(matched_path)
+            return st
+        if isinstance(matched_path, str):
+            st.st_mode = stat.S_IFREG | 0o644
+            st.st_ctime = now
+            st.st_mtime = now
+            st.st_atime = now
+            st.st_uid = uid
+            st.st_gid = gid
+            st.st_size = len(matched_path)
+            st.st_nlink = 1
+            return st
+        if isinstance(matched_path, tuple):
+            st.st_mode = stat.S_IFREG | 0o644
+            st.st_ctime = now
+            st.st_mtime = now
+            st.st_atime = now
+            st.st_uid = uid
+            st.st_gid = gid
+            st.st_size = matched_path[0]()
+            st.st_nlink = 1
+            return st
+        return -errno.ENOENT
+
+    def open(self, path, flags):
+        logger.debug('open %s' % (path,))
+        matched_path = self.match_path(path)
+        if matched_path is None:
+            return -errno.ENOENT
+        for i in range(1, 10):
+            if i not in self.fhs:
+                if isinstance(matched_path, str):
+                    self.fhs[i] = matched_path
+                elif isinstance(matched_path, tuple):
+                    self.fhs[i] = matched_path[1]()
+                else:
+                    raise -errno.EFTYPE
+                return FileHandle(i)
+        raise -errno.ENFILE
+
+    # not done
+    def read(self, path, size, offset, fh):
+        logger.debug('read')
+        logger.debug(path)
+        logger.debug(size)
+        logger.debug(offset)
+        logger.debug(fh)
+        return self.fhs[fh.fno][offset:offset + size]
+
+    def release(self, path, flags, fh):
+        logger.debug('release')
+        logger.debug(path)
+        logger.debug(fh)
+        del self.fhs[fh.fno]
+        return
+
+
+def get_opt_parser():
+    # use module docstring for help output
+    p = OptionParser(
+        usage="%s [OPTIONS] <DIRECTORY CONTAINING DICOMSs> <mount point>"
+              % os.path.basename(sys.argv[0]),
+        version="%prog " + nib.__version__)
+
+    p.add_options([
+        Option("-v", "--verbose", action="count",
+               dest="verbose", default=0,
+               help="make noise.  Could be specified multiple times"),
+    ])
+
+    p.add_options([
+        Option("-L", "--follow-links", action="store_true",
+               dest="followlinks", default=False,
+               help="Follow symbolic links in DICOM directory"),
+    ])
+    return p
+
+
+def main(args=None):
+    parser = get_opt_parser()
+    (opts, files) = parser.parse_args(args=args)
+
+    if opts.verbose:
+        logger.addHandler(logging.StreamHandler(sys.stdout))
+        logger.setLevel(opts.verbose > 1 and logging.DEBUG or logging.INFO)
+
+    if len(files) != 2:
+        sys.stderr.write("Please provide two arguments:\n%s\n" % parser.usage)
+        sys.exit(1)
+
+    fs = DICOMFS(
+        dash_s_do='setsingle',
+        followlinks=opts.followlinks,
+        dicom_path=files[0].decode(encoding)
+    )
+    fs.parse(['-f', '-s', files[1]])
+    try:
+        fs.main()
+    except fuse.FuseError:
+        # fuse prints the error message
+        sys.exit(1)
+
+    sys.exit(0)
diff --git a/nibabel/cmdline/ls.py b/nibabel/cmdline/ls.py
index 98f75e21dc..f919700247 100755
--- a/nibabel/cmdline/ls.py
+++ b/nibabel/cmdline/ls.py
@@ -21,8 +21,7 @@
 import nibabel.cmdline.utils
 from nibabel.cmdline.utils import _err, verbose, table2string, ap, safe_get
 
-__author__ = 'Yaroslav Halchenko'
-__copyright__ = 'Copyright (c) 2011-2016 Yaroslav Halchenko ' \
+__copyright__ = 'Copyright (c) 2011-18 Yaroslav Halchenko ' \
                 'and NiBabel contributors'
 __license__ = 'MIT'
 
@@ -153,11 +152,11 @@ def proc_file(f, opts):
     return row
 
 
-def main():
+def main(args=None):
     """Show must go on"""
 
     parser = get_opt_parser()
-    (opts, files) = parser.parse_args()
+    (opts, files) = parser.parse_args(args=args)
 
     nibabel.cmdline.utils.verbose_level = opts.verbose
 
diff --git a/nibabel/cmdline/nifti_dx.py b/nibabel/cmdline/nifti_dx.py
new file mode 100644
index 0000000000..e478b5a5c2
--- /dev/null
+++ b/nibabel/cmdline/nifti_dx.py
@@ -0,0 +1,38 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+''' Print nifti diagnostics for header files '''
+
+import sys
+from optparse import OptionParser
+
+import nibabel as nib
+
+__author__ = 'Matthew Brett'
+__copyright__ = 'Copyright (c) 2011-18 Matthew Brett ' \
+                'and NiBabel contributors'
+__license__ = 'MIT'
+
+
+def main(args=None):
+    """ Go go team """
+    parser = OptionParser(
+        usage="%s [FILE ...]\n\n" % sys.argv[0] + __doc__,
+        version="%prog " + nib.__version__)
+    (opts, files) = parser.parse_args(args=args)
+
+    for fname in files:
+        with nib.openers.ImageOpener(fname) as fobj:
+            hdr = fobj.read(nib.nifti1.header_dtype.itemsize)
+        result = nib.Nifti1Header.diagnose_binaryblock(hdr)
+        if len(result):
+            print('Picky header check output for "%s"\n' % fname)
+            print(result + '\n')
+        else:
+            print('Header for "%s" is clean' % fname)
diff --git a/nibabel/parrec2nii_cmd.py b/nibabel/cmdline/parrec2nii.py
similarity index 100%
rename from nibabel/parrec2nii_cmd.py
rename to nibabel/cmdline/parrec2nii.py
diff --git a/nibabel/cmdline/tests/__init__.py b/nibabel/cmdline/tests/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/nibabel/tests/test_parrec2nii.py b/nibabel/cmdline/tests/test_parrec2nii.py
similarity index 91%
rename from nibabel/tests/test_parrec2nii.py
rename to nibabel/cmdline/tests/test_parrec2nii.py
index aa018b24d0..c5b5831270 100644
--- a/nibabel/tests/test_parrec2nii.py
+++ b/nibabel/cmdline/tests/test_parrec2nii.py
@@ -6,7 +6,7 @@
 from numpy import array as npa
 
 import nibabel
-from nibabel import parrec2nii_cmd as parrec2nii
+from nibabel.cmdline import parrec2nii
 
 from mock import Mock, MagicMock, patch
 from nose.tools import assert_true
@@ -29,10 +29,10 @@
  [   0.        ,    0.  ,          0.        ,    1.        ]])
 
 
-@patch('nibabel.parrec2nii_cmd.verbose')
-@patch('nibabel.parrec2nii_cmd.io_orientation')
-@patch('nibabel.parrec2nii_cmd.nifti1')
-@patch('nibabel.parrec2nii_cmd.pr')
+@patch('nibabel.cmdline.parrec2nii.verbose')
+@patch('nibabel.cmdline.parrec2nii.io_orientation')
+@patch('nibabel.cmdline.parrec2nii.nifti1')
+@patch('nibabel.cmdline.parrec2nii.pr')
 def test_parrec2nii_sets_qform_sform_code1(*args):
     # Check that set_sform(), set_qform() are called on the new header.
     parrec2nii.verbose.switch = False
@@ -67,7 +67,7 @@ def test_parrec2nii_sets_qform_sform_code1(*args):
     nhdr.set_sform.assert_called_with(AN_OLD_AFFINE, code=1)
 
 
-@patch('nibabel.parrec2nii_cmd.verbose')
+@patch('nibabel.cmdline.parrec2nii.verbose')
 def test_parrec2nii_save_load_qform_code(*args):
     # Tests that after parrec2nii saves file, it has the sform and qform 'code'
     # set to '1', which means 'scanner', so that other software, e.g. FSL picks
diff --git a/nibabel/tests/test_scripts.py b/nibabel/tests/test_scripts.py
index 941e2271b0..cb24f893d2 100644
--- a/nibabel/tests/test_scripts.py
+++ b/nibabel/tests/test_scripts.py
@@ -128,6 +128,25 @@ def test_nib_ls_multiple():
     )
 
 
+@script_test
+def test_help():
+    for cmd in ['parrec2nii', 'nib-dicomfs', 'nib-ls', 'nib-nifti-dx']:
+        if cmd == 'nib-dicomfs':
+            # needs special treatment since depends on fuse module which
+            # might not be available.
+            try:
+                import fuse
+            except Exception:
+                continue  # do not test this one
+        code, stdout, stderr = run_command([cmd, '--help'])
+        assert_equal(code, 0)
+        assert_re_in(".*%s" % cmd, stdout)
+        assert_re_in(".*Usage", stdout)
+        # Some third party modules might like to announce some Deprecation
+        # etc warnings, see e.g. https://travis-ci.org/nipy/nibabel/jobs/370353602
+        if 'warning' not in stderr.lower():
+            assert_equal(stderr, '')
+
 
 @script_test
 def test_nib_nifti_dx():