diff --git a/nbgrader/converters/base.py b/nbgrader/converters/base.py
index c4af98b2..5fabe801 100644
--- a/nbgrader/converters/base.py
+++ b/nbgrader/converters/base.py
@@ -66,7 +66,12 @@ class BaseConverter(LoggingConfigurable):
         self.exporter = self.exporter_class(parent=self, config=self.config)
         for pp in self.preprocessors:
             self.exporter.register_preprocessor(pp)
-        self.convert_notebooks()
+        currdir = os.getcwd()
+        os.chdir(self.coursedir.root)
+        try:
+            self.convert_notebooks()
+        finally:
+            os.chdir(currdir)
 
     @default("classes")
     def _classes_default(self):
diff --git a/nbgrader/preprocessors/headerfooter.py b/nbgrader/preprocessors/headerfooter.py
index 56c5dc27..83c6aaa6 100644
--- a/nbgrader/preprocessors/headerfooter.py
+++ b/nbgrader/preprocessors/headerfooter.py
@@ -8,8 +8,8 @@ from ..nbgraderformat import read as read_nb
 class IncludeHeaderFooter(NbGraderPreprocessor):
     """A preprocessor for adding header and/or footer cells to a notebook."""
 
-    header = Unicode("", help="Path to header notebook").tag(config=True)
-    footer = Unicode("", help="Path to footer notebook").tag(config=True)
+    header = Unicode("", help="Path to header notebook, relative to the root of the course directory").tag(config=True)
+    footer = Unicode("", help="Path to footer notebook, relative to the root of the course directory").tag(config=True)
 
     def preprocess(self, nb, resources):
         """Concatenates the cells from the header and footer notebooks to the

Error generating assignment and managing students
Firstly, I apologize if this is not the proper place to report issues like this.  I am exploring nbgrader, and have had some trouble getting it to work.

I have installed nbgrader on a local Jupyterhub installation and have been working through the example notebooks.

I had to create a `~/.jupyter/nbgrader_config.py` file that has the following contents:
```
c = get_config()
c.CourseDirectory.root = '~/Jupyter/ChEn6703_test_nbgrader'
```
(note that I used the full path above, but replaced the prefix with `~` for security reasons)

There are a few strange things going on though:

## Problems with student entries
1. When I go to the `Manage Students` section of nbgrader, it doesn't show any students.
1. When I do `nbgrader db student list --log-level='DEBUG'` I get something which is inconsistent with the empty list in the `Manage Students` dialog.
```
[DbStudentListApp | DEBUG] Searching ['~/Jupyter/ChEn6703_test_nbgrader', '~/.jupyter', '/usr/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[DbStudentListApp | DEBUG] Looking for jupyter_config in /etc/jupyter
[DbStudentListApp | DEBUG] Looking for jupyter_config in /usr/local/etc/jupyter
[DbStudentListApp | DEBUG] Looking for jupyter_config in /usr/etc/jupyter
[DbStudentListApp | DEBUG] Looking for jupyter_config in ~/.jupyter
[DbStudentListApp | DEBUG] Looking for jupyter_config in ~/Jupyter/ChEn6703_test_nbgrader
[DbStudentListApp | DEBUG] Looking for nbgrader_config in /etc/jupyter
[DbStudentListApp | DEBUG] Looking for nbgrader_config in /usr/local/etc/jupyter
[DbStudentListApp | DEBUG] Looking for nbgrader_config in /usr/etc/jupyter
[DbStudentListApp | DEBUG] Looking for nbgrader_config in ~/.jupyter
[DbStudentListApp | DEBUG] Loaded config file: ~/.jupyter/nbgrader_config.py
[DbStudentListApp | DEBUG] Looking for nbgrader_config in ~/Jupyter/ChEn6703_test_nbgrader
[DbStudentListApp | DEBUG] Loaded config file: ~/Jupyter/ChEn6703_test_nbgrader/nbgrader_conf
ig.py
[DbStudentListApp | DEBUG] Looking for nbgrader_config in ~/Jupyter/ChEn6703_test_nbgrader
[DbStudentListApp | DEBUG] Loaded config file: ~/Jupyter/ChEn6703_test_nbgrader/nbgrader_conf
ig.py
There are 1 students in the database:
1 (Flinstone, Fred) -- None
```
3. If I manually enter a student in the `Manage Students` dialog, the student shows up and then disappears.

## Problems when generating the assignment
When I go to `Manage Assignments` and click on the `Generate` icon for the example `ps1` assignment, I get:
```
[INFO] Copying ~/Jupyter/ChEn6703_test_nbgrader/source/./ps1/jupyter.png -> ~/Jupyter/ChEn6703_test_nbgrader/release/./ps1/jupyter.png
[INFO] Updating/creating assignment 'ps1': {}
[INFO] Converting notebook ~/Jupyter/ChEn6703_test_nbgrader/source/./ps1/problem1.ipynb
[ERROR] There was an error processing assignment: ~/Jupyter/ChEn6703_test_nbgrader/source/./ps1
[ERROR] Traceback (most recent call last):
      File "/usr/local/lib/python3.5/dist-packages/nbgrader/converters/base.py", line 288, in convert_notebooks
        self.convert_single_notebook(notebook_filename)
      File "/usr/local/lib/python3.5/dist-packages/nbgrader/converters/base.py", line 244, in convert_single_notebook
        output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/exporters/exporter.py", line 172, in from_filename
        return self.from_file(f, resources=resources, **kw)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/exporters/exporter.py", line 190, in from_file
        return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/exporters/notebook.py", line 31, in from_notebook_node
        nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/exporters/exporter.py", line 132, in from_notebook_node
        nb_copy, resources = self._preprocess(nb_copy, resources)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/exporters/exporter.py", line 309, in _preprocess
        nbc, resc = preprocessor(nbc, resc)
      File "/usr/local/lib/python3.5/dist-packages/nbconvert/preprocessors/base.py", line 47, in __call__
        return self.preprocess(nb,resources)
      File "/usr/local/lib/python3.5/dist-packages/nbgrader/preprocessors/headerfooter.py", line 23, in preprocess
        with open(self.header, 'r') as fh:
    FileNotFoundError: [Errno 2] No such file or directory: 'source/header.ipynb'
    
[WARNING] Removing failed assignment: ~/Jupyter/ChEn6703_test_nbgrader/release/ps1
[ERROR] There was an error processing assignment 'ps1' for student '.'
[ERROR] Please see the the above traceback for details on the specific errors on the above failures.
Traceback
```
I have tried regenerating the entire class and this issue persists.

If I try the command line approach: `nbgrader assign source/ps1/` I get:
```
[AssignApp | ERROR] No notebooks were matched by ~/Jupyter/ChEn6703_test_nbgrader/source/./s
```
Note the `source/./s` which seems problematic.

Any ideas on this?
diff --git a/nbgrader/tests/apps/test_nbgrader_assign.py b/nbgrader/tests/apps/test_nbgrader_assign.py
index 85539e3e..73575ef2 100644
--- a/nbgrader/tests/apps/test_nbgrader_assign.py
+++ b/nbgrader/tests/apps/test_nbgrader_assign.py
@@ -277,3 +277,15 @@ class TestNbGraderAssign(BaseTestApp):
         run_nbgrader(["assign", "ps1", "--no-db", "--no-metadata"])
         assert os.path.exists(join(course_dir, "release", "ps1", "p1.ipynb"))
 
+    def test_header(self, course_dir):
+        """Does the relative path to the header work?"""
+        self._empty_notebook(join(course_dir, 'source', 'ps1', 'foo.ipynb'))
+        self._empty_notebook(join(course_dir, 'source', 'header.ipynb'))
+        with open("nbgrader_config.py", "a") as fh:
+            fh.write("""c.CourseDirectory.db_assignments = [dict(name="ps1")]\n""")
+            fh.write("""c.IncludeHeaderFooter.header = "source/header.ipynb"\n""")
+        run_nbgrader(["assign", "ps1"])
+        assert os.path.isfile(join(course_dir, "release", "ps1", "foo.ipynb"))
+
+
+

pip install -r dev-requirements.txt -e .
parse_log_pytest
requirements.txt
pytest pytest-cov pytest-rerunfailures coverage selenium invoke sphinx codecov cov-core nbval
pip install -U pip wheel setuptools
3.5
dev-requirements.txt dev-requirements-windows.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
alabaster==0.7.13
alembic==1.7.7
anyio==3.6.2
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
async-generator==1.10
attrs==22.2.0
Babel==2.11.0
backcall==0.2.0
bleach==4.1.0
certifi==2021.5.30
cffi==1.15.1
charset-normalizer==2.0.12
codecov==2.1.13
comm==0.1.4
contextvars==2.4
cov-core==1.15.0
coverage==6.2
dataclasses==0.8
decorator==5.1.1
defusedxml==0.7.1
docutils==0.18.1
entrypoints==0.4
greenlet==2.0.2
idna==3.10
imagesize==1.4.1
immutables==0.19
importlib-metadata==4.8.3
importlib-resources==5.4.0
iniconfig==1.1.1
invoke==2.2.0
ipykernel==5.5.6
ipython==7.16.3
ipython-genutils==0.2.0
ipywidgets==7.8.5
jedi==0.17.2
Jinja2==3.0.3
json5==0.9.16
jsonschema==3.2.0
jupyter==1.1.1
jupyter-client==7.1.2
jupyter-console==6.4.3
jupyter-core==4.9.2
jupyter-server==1.13.1
jupyterlab==3.2.9
jupyterlab-pygments==0.1.2
jupyterlab-server==2.10.3
jupyterlab_widgets==1.1.11
Mako==1.1.6
MarkupSafe==2.0.1
mistune==0.8.4
nbclassic==0.3.5
nbclient==0.5.9
nbconvert==6.0.7
nbformat==5.1.3
-e git+https://github.com/jupyter/nbgrader.git@c647866318ccb67681d832afb8a0579d78fa6786#egg=nbgrader
nbval==0.10.0
nest-asyncio==1.6.0
notebook==6.4.10
packaging==21.3
pandocfilters==1.5.1
parso==0.7.1
pexpect==4.9.0
pickleshare==0.7.5
pluggy==1.0.0
prometheus-client==0.17.1
prompt-toolkit==3.0.36
ptyprocess==0.7.0
py==1.11.0
pycparser==2.21
pyenchant==3.2.2
Pygments==2.14.0
pyparsing==3.1.4
pyrsistent==0.18.0
pytest==7.0.1
pytest-cov==4.0.0
pytest-rerunfailures==10.3
python-dateutil==2.9.0.post0
pytz==2025.2
pyzmq==25.1.2
requests==2.27.1
selenium==3.141.0
Send2Trash==1.8.3
six==1.17.0
sniffio==1.2.0
snowballstemmer==2.2.0
Sphinx==5.3.0
sphinx-rtd-theme==2.0.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jquery==4.1
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
sphinxcontrib-spelling==7.7.0
SQLAlchemy==1.4.54
terminado==0.12.1
testpath==0.6.0
tomli==1.2.3
tornado==6.1
traitlets==4.3.3
typing_extensions==4.1.1
urllib3==1.26.20
wcwidth==0.2.13
webencodings==0.5.1
websocket-client==1.3.1
widgetsnbextension==3.6.10
zipp==3.6.0

name: nbgrader
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2021.5.30=py36h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - python=3.6.13=h12debd9_1
  - readline=8.2=h5eee18b_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - alabaster==0.7.13
      - alembic==1.7.7
      - anyio==3.6.2
      - argon2-cffi==21.3.0
      - argon2-cffi-bindings==21.2.0
      - async-generator==1.10
      - attrs==22.2.0
      - babel==2.11.0
      - backcall==0.2.0
      - bleach==4.1.0
      - cffi==1.15.1
      - charset-normalizer==2.0.12
      - codecov==2.1.13
      - comm==0.1.4
      - contextvars==2.4
      - cov-core==1.15.0
      - coverage==6.2
      - dataclasses==0.8
      - decorator==5.1.1
      - defusedxml==0.7.1
      - docutils==0.18.1
      - entrypoints==0.4
      - greenlet==2.0.2
      - idna==3.10
      - imagesize==1.4.1
      - immutables==0.19
      - importlib-metadata==4.8.3
      - importlib-resources==5.4.0
      - iniconfig==1.1.1
      - invoke==2.2.0
      - ipykernel==5.5.6
      - ipython==7.16.3
      - ipython-genutils==0.2.0
      - ipywidgets==7.8.5
      - jedi==0.17.2
      - jinja2==3.0.3
      - json5==0.9.16
      - jsonschema==3.2.0
      - jupyter==1.1.1
      - jupyter-client==7.1.2
      - jupyter-console==6.4.3
      - jupyter-core==4.9.2
      - jupyter-server==1.13.1
      - jupyterlab==3.2.9
      - jupyterlab-pygments==0.1.2
      - jupyterlab-server==2.10.3
      - jupyterlab-widgets==1.1.11
      - mako==1.1.6
      - markupsafe==2.0.1
      - mistune==0.8.4
      - nbclassic==0.3.5
      - nbclient==0.5.9
      - nbconvert==6.0.7
      - nbformat==5.1.3
      - nbval==0.10.0
      - nest-asyncio==1.6.0
      - notebook==6.4.10
      - packaging==21.3
      - pandocfilters==1.5.1
      - parso==0.7.1
      - pexpect==4.9.0
      - pickleshare==0.7.5
      - pip==21.3.1
      - pluggy==1.0.0
      - prometheus-client==0.17.1
      - prompt-toolkit==3.0.36
      - ptyprocess==0.7.0
      - py==1.11.0
      - pycparser==2.21
      - pyenchant==3.2.2
      - pygments==2.14.0
      - pyparsing==3.1.4
      - pyrsistent==0.18.0
      - pytest==7.0.1
      - pytest-cov==4.0.0
      - pytest-rerunfailures==10.3
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - pyzmq==25.1.2
      - requests==2.27.1
      - selenium==3.141.0
      - send2trash==1.8.3
      - setuptools==59.6.0
      - six==1.17.0
      - sniffio==1.2.0
      - snowballstemmer==2.2.0
      - sphinx==5.3.0
      - sphinx-rtd-theme==2.0.0
      - sphinxcontrib-applehelp==1.0.2
      - sphinxcontrib-devhelp==1.0.2
      - sphinxcontrib-htmlhelp==2.0.0
      - sphinxcontrib-jquery==4.1
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==1.0.3
      - sphinxcontrib-serializinghtml==1.1.5
      - sphinxcontrib-spelling==7.7.0
      - sqlalchemy==1.4.54
      - terminado==0.12.1
      - testpath==0.6.0
      - tomli==1.2.3
      - tornado==6.1
      - traitlets==4.3.3
      - typing-extensions==4.1.1
      - urllib3==1.26.20
      - wcwidth==0.2.13
      - webencodings==0.5.1
      - websocket-client==1.3.1
      - widgetsnbextension==3.6.10
      - zipp==3.6.0
prefix: /opt/conda/envs/nbgrader

nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_header
nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_help nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_no_args nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_conflicting_args nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_multiple_args nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_no_assignment nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_single_file nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_multiple_files nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_dependent_files nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_save_cells nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_force nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_permissions nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_custom_permissions nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_add_remove_extra_notebooks nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_add_extra_notebooks_with_submissions nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_remove_extra_notebooks_with_submissions nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_same_notebooks_with_submissions nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_force_single_notebook nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_fail_no_notebooks nbgrader/tests/apps/test_nbgrader_assign.py::TestNbGraderAssign::test_no_metadata
nbgrader/converters/base.py nbgrader/preprocessors/headerfooter.py
nbgrader/converters/base.py nbgrader/preprocessors/headerfooter.py