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]NOTE: This program is now superseded by SurfToSurf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
- [-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: http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm
If you can’t get help here, please get help somewhere.
Dec 16 2015
Shruti Japee LBC/NIMH/NIH shruti@codon.nih.gov Ziad S. Saad SSSC/NIMH/NIH saadz@mail.nih.gov