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'''Synopsis''' - Minimal command invocation which does not use options. '''Synopsis''' - Command usage. Options should be placed in square brackets, e.g., mri_info [-m] [-o outputfile]. If there are too many options then use the placeholder <options>, e.g., mri_info <options>
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'''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. '''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.
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'''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.  '''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.
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'''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.  '''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.

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, e.g., mri_info [-m] [-o outputfile]. If there are too many options then use the placeholder <options>, e.g., mri_info <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 and description of volumes ouput by the command.

Description - Detailed description of command including relevant concepts.

Examples - Commonly used examples for the commands.

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

See Also - Related commands in FreeSurfer.

Links - Relevant links on FreeSurferWiki.

Methods Description - Description of command which would be suitable for publication in a manuscript. As much as possible, the text should be copy-and-pastable into the Methods section of the 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.

Author/s - Author/s of command.

HelpOnCommandTemplate (last edited 2008-04-29 11:45:22 by localhost)