This page provides a description of the headings in the CommandTemplate. Adherence to the this format helps maintain a consistent style specification across all of the commands in FreeSurfer.

(To actually use a template to create a new page, see comments at bottom. -- GW)

Name - Name of command followed by a dash (-) followed by a very brief summary. Eg, mri_info - provides informtion about volume.

Synopsis - Command usage. Arguments should be enclosed in angular brackets and options should be enclosed in square brackets. For example, in mri_info -i <inputfile> -o <outputfile> [-m], <inputfile> and <outputfile> are arguments and -m is an optional flag.. If there are too many options then use the placeholder [options], e.g., mri_info -i <inputfile> -o <outputfile> [options]

Arguments

• Positional Arguments - Positional arguments are arguments which are specified by their place in the command string, as opposed to being specified by a flag. Eg, in "mri_convert f g" f and g are positional arguments since they are not passed as arguments of flags. The Positional Arguments field should include a very brief summary followed by a more detailed summary. The brief summary can be a sentence fragment which describes the function of the argument, and the more detailed description can provide additional information which you may find in a help file. The brief and detailed summaries are placed in different table cells using the vertical pipe || formatting.

  Required Flagged Arguments - Flagged arugments which are required. The Required Flagged Arguments field should include a very brief summary followed by a more detailed summary. The brief and detailed summaries are placed in different table cells using the vertical pipe || formatting.

  Optional Flagged Arguments - Flagged arguments which are not required. The Optional Flagged Arguments field should include a very brief summary followed by a more detailed summary. The brief and detailed summaries are placed in different table cells using the vertical pipe || formatting.

Outputs - Name, description, and file format of volumes ouput by the command.

Description - Detailed description of command including relevant concepts.

Examples

• Example 1 - Example of common usage for command.

  Example 2 - Example with more options.

Bugs - Known bugs. Note that bugs should not be reported here. Rather, bug reports should be sent to the relevant support line.

See Also - Related commands in FreeSurfer.

Links - Relevant links on FreeSurferWiki. Useful for providing links to concepts.

Methods Description - Description of command which would be suitable for publication in a scientific manuscript. As much as possible, the text should be copy-and-pastable into the Methods section of a manuscript. This section should be written in past tense to conform to the style of a scientific manuscript. No Wiki formmating should be used in this section.

References - Relevant references. The reference can be posted in the References section.

Reporting Bugs - Where to report bugs. See FreeSurferSupport.

Author/s - Author/s of command. The Author name should be the author's WikiUserName. In Unix, you can see who last modified a command by typing ls -l `which COMMMAND` where COMMAND is the name of the command.

Create new page from template

1. Perform any procedure that provokes moin moin to offer to create a new page. For example, on an existing page, insert the wiki page name of the new page you want to create (which will become a link to your new page). This is described here: HelpForBeginners, but basically you insert a name with embedded capitals like this: MyNewPage. Save and then view this existing page.

2. When viewing the just-edited existing page, your new wiki page name will not yet perform as a link (because as yet the new page has not been created) but will have a question mark "?" link beside it. Clicking on that "?" will invoke a page that offers to create your new page from scratch, or from a list of template pages. Click on one of the template links (for example CommandTemplate) to create your new template-based page.

-- GW