DOC: Various fixes and inclusion of lonely files.

mih · mih · commit 21cb66c57c37 · 2010-10-13T10:17:28.000-04:00
Docs now build without warning.
diff --git a/doc/source/api.rst b/doc/source/api.rst
@@ -21,11 +21,11 @@ File Formats
    :toctree: generated
 
    analyze
-   dicom
    spm2analyze
    spm99analyze
    gifti
    minc
+   nicom
    nifti1
    parrec
    trackvis
diff --git a/doc/source/dicom/dcm2nii_algorithms.rst b/doc/source/dicom/dcm2nii_algorithms.rst
@@ -7,7 +7,9 @@
 dcm2nii_ is an open source DICOM_ to nifti_ conversion program, written
 by Chris Rorden, in Delphi (object orientated pascal).  It's part of
 Chris' popular mricron_ collection of programs.  The source appears to
-be best found on the mricron nitrc_ site.  It's BSD_ licensed. 
+be best found on the `mricron NITRC site`_.  It's BSD_ licensed. 
+
+.. _mricron NITRC site: http://www.nitrc.org/projects/mricron
 
 These are working notes looking at Chris' algorithms for working with
 DICOM.
diff --git a/doc/source/dicom/dicom.rst b/doc/source/dicom/dicom.rst
@@ -15,3 +15,4 @@ Contents:
    dicom_mosaic
    siemens_csa
    spm_dicom
+   dcm2nii_algorithms
diff --git a/doc/source/gitwash/index.rst b/doc/source/gitwash/index.rst
@@ -13,6 +13,7 @@ Contents:
    following_latest
    patching
    git_development
+   dot2_dot3
    git_resources
 
 
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -75,4 +75,5 @@ search* located in the sidebar of the NiBabel home page.
 
    manual
    devguide
+   devdiscuss
    api
diff --git a/doc/source/manual.rst b/doc/source/manual.rst
@@ -8,6 +8,7 @@ NiBabel Manual
 
   installation
   gettingstarted
+  installing_data
   dicom/dicom
   legal
   changelog
diff --git a/nibabel/__init__.py b/nibabel/__init__.py
@@ -11,8 +11,8 @@
 
 from .info import __version__, long_description as __doc__
 __doc__ += """
- Quickstart
-============
+Quickstart
+==========
 
 ::
 
@@ -31,6 +31,8 @@
 
    new_image = nib.Nifti1Image(data, affine)
    nib.save(new_image, 'new_image.nii.gz')
+
+For more detailed information see the :ref:`manual`.
 """
 # module imports
 from . import analyze as ana
