|
Size: 2578
Comment: new page
|
Size: 2898
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 5: | Line 5: |
| '''Synopsis''' - Minimal command invocation which does not use options. | '''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. |
| Line 7: | Line 7: |
| '''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. |
| Line 9: | Line 10: |
| '''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. |
| Line 11: | Line 12: |
| '''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. |
| Line 13: | Line 14: |
| '''Outputs''' - Name and description of volumes ouput by the command. | '''Outputs''' - Name, description, and file format of volumes ouput by the command. |
| Line 15: | Line 16: |
| '''Description''' - Description of command. | '''Description''' - Detailed description of command including relevant concepts. |
| Line 17: | Line 18: |
| '''Examples''' - Commonly used examples for the commands. | '''Examples''' '''Example 1''' - Example of common usage for command. |
| Line 19: | Line 21: |
| '''Bugs''' - Known bugs. Note that bugs should not be reported here by users. Rather, bug reports should be addressed to the relevant support line. None |
'''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. |
| Line 24: | Line 27: |
| '''Links''' - Relecant links on FreeSurferWiki. | '''Links''' - Relevant links on FreeSurferWiki. |
| Line 32: | Line 35: |
| '''Author/s''' - Author/s of command. | '''Author/s''' - Author/s of command. |
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.
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.