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.
Name - Name of command followed by a dash (-) followed by a very brief summary. Eg, mri_info - provides informtion about volume.
Synopsis - Command usage. Options should be placed in square brackets and required arguments should just be written as text, e.g., mri_info [-m] [-o outputfile] inputfile. If there are too many options then use the placeholder <options>, e.g., mri_info <options> inputfile.
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. In Unix, you can see who last modified a command by typing ls -l `which COMMMAND` where COMMAND is the name of the command.