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commit d2bb290d801fcd775416b4b1b8da3f25cb3b0947 Author: Emily Ruzich <[email protected]> Date: Thu Mar 31 12:24:29 2011 -0400 fixing manual --- doc/source/manual/AppA.rst | 2 +- doc/source/manual/AppB.rst | 4 +-- doc/source/manual/AppReleaseNotes.rst | 56 +++++++++++++++++------------------ 3 files changed, 31 insertions(+), 31 deletions(-) diff --git a/doc/source/manual/AppA.rst b/doc/source/manual/AppA.rst index c8a88b4..2b14ea8 100755 --- a/doc/source/manual/AppA.rst +++ b/doc/source/manual/AppA.rst @@ -374,4 +374,4 @@ is: .. note:: If left and right are flipped in BrainSuite, use the --flip option in mne_convert_surface to set the coordinate transformation correctly. -.. note:: The BrainSuite scalp surface can be also used for visualization in mne_analyze , see Section 7.16.1. +.. note:: The BrainSuite scalp surface can be also used for visualization in mne_analyze , see :ref:`CHDCGHIF`. diff --git a/doc/source/manual/AppB.rst b/doc/source/manual/AppB.rst index 682f73e..b77a749 100755 --- a/doc/source/manual/AppB.rst +++ b/doc/source/manual/AppB.rst @@ -127,7 +127,7 @@ This chapter contains information about the options accepted by the program mne_compute_mne , which is gradually becoming obsolete. All of its functions will be eventually included to mne_make_movie , -see Section 6.5. At this time, mne_compute_mne is +see :ref:`CBBECEDE`. At this time, mne_compute_mne is still needed to produce time-collapsed w files unless you are willing to write a Matlab script of your own for this purpose. @@ -256,7 +256,7 @@ the following command-line options: **\---pred <name>** Save the predicted data into this file. This is a fif file containing - the predicted data waveforms, see Section 6.2.7. + the predicted data waveforms, see :ref:`CHDCACDC`. **\---outputnorm <name>** diff --git a/doc/source/manual/AppReleaseNotes.rst b/doc/source/manual/AppReleaseNotes.rst index 106f2b4..49fc87a 100755 --- a/doc/source/manual/AppReleaseNotes.rst +++ b/doc/source/manual/AppReleaseNotes.rst @@ -30,7 +30,7 @@ The following overall changes have been made: of Neuromag software was written. - The MEG sensor information is now imported from the coil definition file - instead of being hardcoded in the software. For details, see Section 5.8.4. + instead of being hardcoded in the software. For details, see :ref:`BJECIGEB`. - CTF and 4D Neuroimaging sensors are now supported. @@ -77,9 +77,9 @@ The following changes have been made in mne_analyze : now supported. - An iterative coordinate alignment procedure was added, see - Section 7.16. + :ref:`CACEHGCD`. -- Utility to view continuous HPI information was added, see Section 7.17. +- Utility to view continuous HPI information was added, see :ref:`CACIADAI`. - Several small changes and bug fixes were done. @@ -164,24 +164,24 @@ The following new features have been added: - Sketchy surface display mode for source spaces with selection triangulation information created with the ``--ico`` option - to mne_setup_source_space . + to mne_setup_source_space. - Rotation of the coordinate frame in the coordinate system - alignment dialog, see Section 7.16; + alignment dialog, see :ref:`CACEHGCD`. - Several new graphics output file formats as well as automatic - and snapshot output modes, see Section 7.8.8. + and snapshot output modes, see :ref:`CACIJFII`. - It is now possible to inquire timecourses from stc overlays. Both labels and surface picking are supported. - Added an option to include surface vertex numbers to the timecourse output, - see Section 7.13.3.1. + see :ref:`CACJJGFA`. -- Overlays matching the scalp surface can now be loaded, see Section 7.14. +- Overlays matching the scalp surface can now be loaded, see :ref:`CACFCHEC`. - The dipole display dialog has now control over the dipole - display properties. Multiple dipoles can be now displayed, see Section 7.15.3. + display properties. Multiple dipoles can be now displayed, see :ref:`CACGGAIA`. - Time stepping with cursor keys has been added. @@ -200,7 +200,7 @@ frames is now included in the output file. mne_make_movie ============== -Added the ``--labelverts`` option, see Section 6.5.8. +Added the ``--labelverts`` option, see :ref:`CBBHHCEF`. mne_surf2bem ============ @@ -208,7 +208,7 @@ mne_surf2bem Added the ``--shift`` option to move surface vertices outwards. Fixed some loopholes in topology checks. Also added the ``--innershift`` option to mne_setup_forward_model . For -more information, see :ref:`CIHDBFEG` and Section 5.6. +more information, see :ref:`CIHDBFEG` and :ref:`BEHCACCJ`. mne_forward_solution ==================== @@ -236,7 +236,7 @@ The following changes have been made in mne_inverse_operator : mne_compute_raw_inverse ======================= -This utility is now documented in Section 6.6. The +This utility is now documented in :ref:`CBBCGHAH`. The utility mne_make_raw_inverse_operator has been removed from the software. @@ -394,10 +394,10 @@ New features include: or trackball. - Added remote control of the FreeSurfer MRI - viewer (tkmedit ), see Section 7.18. + viewer (tkmedit ), see :ref:`CACCHCBF`. - Added fitting of single equivalent current dipoles and channel - selections, see Section 7.15. + selections, see :ref:`CHDGHIJJ`. - Added loading of FreeSurfer cortical parcellation data as labels. @@ -411,12 +411,12 @@ New features include: - A shortcut button to direct a file selector to the appropriate default directory was added to several file loading dialogs. -- The vertex coordinates can now be displayed, see Section 7.8.4. +- The vertex coordinates can now be displayed, see :ref:`CHDIEHDH`. mne_average_forward_solutions ----------------------------- -EEG forward solutions are now averaged as well, see Section 5.10. +EEG forward solutions are now averaged as well, see :ref:`CHDBBFCA`. mne_browse_raw and mne_process_raw ---------------------------------- @@ -516,7 +516,7 @@ mne_compute_raw_inverse ----------------------- The ``--digtrig`` , ``--extra`` , ``--noextra`` , ``--split`` , ``--labeldir`` , and ``--out`` options -were added, see Section 6.6. +were added, see :ref:`CBBCGHAH`. mne_convert_surface ------------------- @@ -545,7 +545,7 @@ mne_forward_solution -------------------- Added code to compute the derivatives of with respect to -the dipole position coordinates, see Section 5.9. +the dipole position coordinates, see :ref:`CHDDIBAH`. mne_list_bem ------------ @@ -563,7 +563,7 @@ mne_make_movie -------------- Added the --noscalebar, --nocomments, --morphgrade, --rate, -and --pickrange options, see Section 6.5. +and --pickrange options, see :ref:`CBBECEDE`. mne_make_source_space --------------------- @@ -572,7 +572,7 @@ The ``--spacing`` option is now implemented in this program, which means mne_mris_trix is now obsolete. The mne_setup_source_space script was modified accordingly. Support for tri, dec, and dip files was dropped, -see Section 5.4. +see :ref:`BEHCGJDD`. mne_mdip2stc ------------ @@ -665,7 +665,7 @@ an MRI overlay, see Section 9.4. mne_volume_source_space ----------------------- -Create a a grid of source points within a volume, see Section 5.5. mne_volume_source_space also +Create a a grid of source points within a volume, see :ref:`BJEFEHJI`. mne_volume_source_space also optionally creates a trilinear interpolator matrix to facilitate converting values a distribution in the volume grid into an MRI overlay using mne_volume_data2mri , @@ -747,7 +747,7 @@ mne_analyze =========== - Both hemispheres can now be displayed - simultaneously, see Section 7.8.3. + simultaneously, see :ref:`CACCABEA`. - If the source space was created with mne_make_source_space version 2.3 or later, the subject's surface data are automatically @@ -772,7 +772,7 @@ Miscellaneous For details, try mne_check_surface --help. - mne_compute_raw_inverse now - has the --orignames option, see Section 6.6.1. + has the --orignames option, see :ref:`CHDEIHFA`. - Added --headcoord option to mne_convert_dig_data , see Section 9.3. @@ -781,7 +781,7 @@ Miscellaneous see Section 9.8. - Added the --morph option to mne_setup_source_space and mne_make_source_space , - see :ref:`CIHCHDAE` and Section 5.4, respectively. + see :ref:`CIHCHDAE` and :ref:`BEHCGJDD`, respectively. - Added the --prefix option to mne_morph_labels , see Section 8.5. @@ -804,9 +804,9 @@ mne_analyze =========== - Added a new restricted mode for visualizing - head position within the helmet, see Sections 7.2 and 7.21. + head position within the helmet, see :ref:`CHDJECCG` and Section 7.21.**doesn't exist** -- Added information about mne_make_scalp_surfaces to Section 7.16.1. +- Added information about mne_make_scalp_surfaces to :ref:`CHDCGHIF`. mne_browse_raw ============== @@ -843,10 +843,10 @@ Miscellaneous see Section 9.7.1. - Added --alpha option to mne_make_movie , - see Section 6.5.5. + see :ref:`CBBBBHIF`. - Added --noiserank option to mne_inverse_operator and mne_do_inverse_operator , - see Sections 6.4 and 3.13, respectively. + see :ref:`CBBDDBGF`and Section 3.13, respectively. - The fif output from mne_convert_dig_data now includes the transformation between the digitizer and MNE head coordinate -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
