diff --git a/doc/source/command_line_tutorial.rst b/doc/source/command_line_tutorial.rst index c3be87a43c0..b66b2a224d7 100644 --- a/doc/source/command_line_tutorial.rst +++ b/doc/source/command_line_tutorial.rst @@ -21,7 +21,7 @@ Build your source space:: Prepare for forward computation:: - # For homegenious volume conductor + # For homogeneous volume conductor mne_setup_forward_model --homog --surf --ico 4 # or for XXX diff --git a/doc/source/manual/AppInstall.rst b/doc/source/manual/AppInstall.rst index 8befa0a9aaf..ec35defa4f8 100644 --- a/doc/source/manual/AppInstall.rst +++ b/doc/source/manual/AppInstall.rst @@ -89,7 +89,7 @@ need to install the netpbm package. The recommended way to do this is to use the MacPorts Project tools, see http://www.macports.org/: - If you have not installed the MacPorts - sofware, goto http://www.macports.org/install.php and follow the + software, goto http://www.macports.org/install.php and follow the instructions to install MacPorts. - Install the netpbm package by saying: ``sudo port install netpbm`` diff --git a/doc/source/manual/cookbook.rst b/doc/source/manual/cookbook.rst index dbb16e2d375..cf19a29046d 100644 --- a/doc/source/manual/cookbook.rst +++ b/doc/source/manual/cookbook.rst @@ -64,7 +64,7 @@ MRI viewer, MRIlab, can be used to access the MRI slice data created by FreeSurfer . In addition, the Neuromag MRI directories can be used for storing the MEG/MRI coordinate transformations created with mne_analyze , -see :ref:`CACEHGCD`. Doring the computation of the forward +see :ref:`CACEHGCD`. During the computation of the forward solution, mne_do_forwand_solution searches for the MEG/MRI coordinate in the Neuromag MRI directories, see :ref:`BABCHEJD`. The fif files created by mne_setup_mrit can be loaded into Matlab with the fiff_read_mri function, @@ -78,7 +78,7 @@ by default they are T1 and brain. This default can be changed by specifying the sets by one or more ``--mri`` options. The script creates the directories ``mri/`` <*name*> ``-neuromag/slices`` and ``mri/`` <*name*> ``-neuromag/sets`` . -If the the input data set is in COR format, mne_setup_mri makes +If the input data set is in COR format, mne_setup_mri makes symbolic links from the COR files in the directory ``mri/`` <*name*> into ``mri/`` <*name*> ``-neuromag/slices`` , and creates a corresponding fif file COR.fif in ``mri/`` <*name*> ``-neuromag/sets`` .. This "description file" contains references to @@ -324,7 +324,7 @@ the forward solutions: This step assigns the conductivity values to the BEM compartments. For the scalp and the brain compartments, the default is 0.3 S/m. -The defalt skull conductivity is 50 times smaller, *i.e.*, +The default skull conductivity is 50 times smaller, *i.e.*, 0.006 S/m. Recent publications, see :ref:`CEGEGDEI`, report a range of skull conductivity ratios ranging from 1:15 (Oostendorp *et al.*, 2000) to 1:25 - 1:50 (Slew *et al.*, diff --git a/doc/source/manual/forward.rst b/doc/source/manual/forward.rst index 4a0a5bb4bd7..793137f87cc 100644 --- a/doc/source/manual/forward.rst +++ b/doc/source/manual/forward.rst @@ -1327,9 +1327,9 @@ the following command-line options: **\---fwd <*name*> :[ <*weight*> ]** Specifies a forward solution to include. If no weight is specified, - 1.0 is asssumed. In the averaging process the weights are divided + 1.0 is assumed. In the averaging process the weights are divided by their sum. For example, if two forward solutions are averaged - and their spefied weights are 2 and 3, the average is formed with + and their specified weights are 2 and 3, the average is formed with a weight of 2/5 for the first solution and 3/5 for the second one. **\---out <*name*>** diff --git a/doc/source/manual/intro.rst b/doc/source/manual/intro.rst index cbbac5ed63d..e0ea63d1d6f 100644 --- a/doc/source/manual/intro.rst +++ b/doc/source/manual/intro.rst @@ -10,7 +10,7 @@ This document describes a set of programs for preprocessing and averaging of MEG and EEG data and for constructing cortically-constrained minimum-norm estimates. This software package will in the sequel be referred to as *MNE software*. The software is based on anatomical -MRI processing, forward modelling, and source estimation methods published in +MRI processing, forward modeling, and source estimation methods published in Dale, Fischl, Hämäläinen, and others. The software depends on anatomical MRI processing tools provided by the FreeSurfer software. diff --git a/doc/source/manual/matlab.rst b/doc/source/manual/matlab.rst index 1d507362078..c13734561df 100644 --- a/doc/source/manual/matlab.rst +++ b/doc/source/manual/matlab.rst @@ -28,8 +28,8 @@ takes place: setup lines are there, nothing happens. A summary of the available routines is provided in Tables :ref:`BGBCGHAG` - :ref:`BGBEFADJ`. The toolbox -also contains a set of examples which may be usedful starting points -for your own development. The names of these functions startwith mne_ex and +also contains a set of examples which may be useful starting points +for your own development. The names of these functions start with mne_ex and they are listed in :ref:`BGBEFADJ`. .. note:: The MNE Matlab Toolbox is compatible with Matlab versions 7.0 or later. @@ -452,7 +452,7 @@ they are listed in :ref:`BGBEFADJ`. +--------------------------------+--------------------------------------------------------------+ -.. note:: In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called *processing history* block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enchanced to include these data to the output file as appropriate. If you have older raw data files created in Matlab from input which has been processed Maxfilter, it is necessary to copy the *processing history* block from the original to modified raw data file using the mne_copy_processing_history utility described in :ref:`CJACECAH`. The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the processing history since revision 2.5 of the MNE software. +.. note:: In order for the inverse operator calculation to work correctly with data processed with the Elekta-Neuromag Maxfilter (TM) software, the so-called *processing history* block must be included in data files. Previous versions of the MNE Matlab functions did not copy processing history to files saved. As of March 30, 2009, the Matlab toolbox routines fiff_start_writing_raw and fiff_write_evoked have been enhanced to include these data to the output file as appropriate. If you have older raw data files created in Matlab from input which has been processed Maxfilter, it is necessary to copy the *processing history* block from the original to modified raw data file using the mne_copy_processing_history utility described in :ref:`CJACECAH`. The raw data processing programs mne_browse_raw and mne_process_raw have handled copying of the processing history since revision 2.5 of the MNE software. Some data structures #################### diff --git a/doc/source/manual/mne.rst b/doc/source/manual/mne.rst index b99d62a0887..ae453b65c8e 100644 --- a/doc/source/manual/mne.rst +++ b/doc/source/manual/mne.rst @@ -165,7 +165,7 @@ be adjusted with the regularization options ``--magreg`` , ``--gradreg`` , and ``--eegreg`` specified at the time of the inverse operator decomposition, see :ref:`CBBDDBGF`. The convenience script mne_do_inverse_solution has the ``--magreg`` and ``--gradreg`` combined to -a sigle option, ``--megreg`` , see :ref:`CIHCFJEI`. +a single option, ``--megreg`` , see :ref:`CIHCFJEI`. Suggested range of values for :math:`\varepsilon_k` is :math:`0.05 \dotso 0.2`. .. _CHDBEHBC: