## Note: This page was created with the CommandTemplate
##
## If you're modifying this page please take a look at the
## latest version of CommandTemplate to ensure that you're
## using the latest version of the CommandTemplate
##
## See HelpOnCommandTemplate for description of formatting

'''Index'''
<<TableOfContents>>


= Name =
mris_fix_topology 

= Synopsis =
mris_fix_topology [options] <subject name> <hemisphere>

= Arguments =
== Positional Arguments ==
|| <subject name> || subject name ||
|| <hemisphere> || hemisphere||

== Required Flagged Arguments ==
none

== Optional Flagged Arguments ==
||-orig origname || ||
||-sphere spherename || ||
||-inflated inflatedname || ||
||-wi || write fixed inflated ||
||-verbose || ||
||-verbose_low || ||
||-warnings || ||
||-errors || ||
||-movies || ||
||-intersect || check if the final surface self-intersects ||
||-mappings || generate several different mappings ||
||-correct_defect N || correct defect N only ||
||-niters N || stop genetic algorithm after N iterations ||
||-genetic || use genetic search ||
||-ga || optimize genetic search ||
||-optimize || optimize genetic search ||
||-random N || use random search with N iterations ||
||-seed N || set random number generator seed to N ||
||-diag || sets DIAG_SAVE_DIAGS ||
||-mgz || assume volumes are in mgz format ||
||-s N || smooth corrected surface by N iterations ||
||-v D || set diagnostic level to D ||
||-help || print help and exit ||
||-version || print version and exit ||

= Description =
This program computes a mapping from the unit sphere onto the surface of the cortex from a previously generated approximation of the cortical surface, thus guaranteeing a topologically correct surface.  

= Examples =
== Example 1 ==
??

== Example 2 ==
??

= Bugs =
none

= See Also =
[[othercommand1]], [[othercommand2]]

= Links =
FreeSurfer

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =
BruceFischl