-debug DBG: if DBG = 2, show dset->ngr in its entirety in NIML form.
- SUMA dataset input options:
- -input DSET: Read DSET1 as input.
In programs accepting multiple input datasets you can use -input DSET1 -input DSET2 or input DSET1 DSET2 ...
- NOTE: Selecting subsets of a dataset:
Much like in AFNI, you can select subsets of a dataset by adding qualifiers to DSET.Append #SEL# to select certain nodes. Append [SEL] to select certain columns. Append {SEL} to select certain rows. The format of SEL is the same as in AFNI, see section:
‘INPUT DATASET NAMES’ in 3dcalc -help for details. Append [i] to get the node index column from
a niml formatted dataset.
- SUMA does not preserve the selection order for any of the selectors. For example: dset[44,10..20] is the same as dset[10..20,44] Also, duplicate values are not supported. so dset[13, 13] is the same as dset[13]. I am not proud of these limitations, someday I’ll get around to fixing them.
- [-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.
Dec 16 2015
Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov