Usage: CompareSurfaces
-spec <Spec file>
-hemi <L or R>
-sv1 <volparentaligned1.BRIK>
-sv2 <volparentaligned2.BRIK>
[-prefix <fileprefix>]
NOTE: This program is now superseded by SurfToSurf
This program calculates the distance, at each node in Surface 1 (S1) to Surface 2 (S2)
The distances are computed along the local surface normal at each node in S1.
S1 and S2 are the first and second surfaces encountered in the spec file, respectively.
-spec <Spec file>: File containing surface specification. This file is typically
generated by @SUMA_Make_Spec_FS (for FreeSurfer surfaces) or
@SUMA_Make_Spec_SF (for SureFit surfaces).
-hemi <left or right>: specify the hemisphere being processed
-sv1 <volume parent BRIK>:volume parent BRIK for first surface
-sv2 <volume parent BRIK>:volume parent BRIK for second surface
Optional parameters:
[-prefix <fileprefix>]: Prefix for distance and node color output files.
Existing file will not be overwritten.
[-onenode <index>]: output results for node index only.
This option is for debugging.
[-noderange <istart> <istop>]: output results from node istart to node istop only.
This option is for debugging.
NOTE: -noderange and -onenode are mutually exclusive
[-nocons]: Skip mesh orientation consistency check.
This speeds up the start time so it is useful
for debugging runs.
[-novolreg]: Ignore any Rotate, Volreg, Tagalign,
or WarpDrive transformations present in
the Surface Volume.
[-noxform]: Same as -novolreg
[-setenv "'ENVname=ENVvalue'"]: Set environment variable ENVname
to be ENVvalue. Quotes are necessary.
Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'"
See also options -update_env, -environment, etc
in the output of 'suma -help'
Common Debugging Options:
[-trace]: Turns on In/Out debug and Memory tracing.
For speeding up the tracing log, I recommend
you redirect stdout to a file when using this option.
For example, if you were running suma you would use:
suma -spec lh.spec -sv ... > TraceFile
This option replaces the old -iodbg and -memdbg.
[-TRACE]: Turns on extreme tracing.
[-nomall]: Turn off memory tracing.
[-yesmall]: Turn on memory tracing (default).
NOTE: For programs that output results to stdout
(that is to your shell/screen), the debugging info
might get mixed up with your results.
Global Options (available to all AFNI/SUMA programs)
-h: Mini help, at time, same as -help in many cases.
-help: The entire help output
-HELP: Extreme help, same as -help in majority of cases.
-h_view: Open help in text editor. AFNI will try to find a GUI editor
-hview : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_web: Open help in web browser. AFNI will try to find a browser.
-hweb : on your machine. You can control which it should use by
setting environment variable AFNI_GUI_EDITOR.
-h_find WORD: Look for lines in this programs's -help output that match
(approximately) WORD.
-h_raw: Help string unedited
-h_spx: Help string in sphinx loveliness, but do not try to autoformat
-h_aspx: Help string in sphinx with autoformatting of options, etc.
-all_opts: Try to identify all options for the program from the
output of its -help option. Some options might be missed
and others misidentified. Use this output for hints only.
For more help: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/SUMA/main_toc.html
If you can't get help here, please get help somewhere.
Compile Date:
Oct 13 2022
Shruti Japee LBC/NIMH/NIH shruti@codon.nih.gov Ziad S. Saad SSSC/NIMH/NIH saadz@mail.nih.gov
