SYNOPSIS
view_sm -analysis analysis_name -positive # -negative # -sf sessid -df sessdir [-frac # -type # -funcdir -help -man -debug]
Type ``view_sm -man'' for complete documentation
DESCRIPTION
Selectivity indices provide a means for determining the ``selectivity'' of particular voxels. In this case, selectivity means a measure of how much a voxel responds to one condition (denoted here as the ``positive'' condition) versus another condition (denoted here as the ``negative'' condition). While statistical maps provide a description of areas that are active versus another condition, selectivity maps (and the corresponding indices) provide a description of how well a voxel is tuned for a particular condition.
Consistent formulas for determining selectivity are not present in the literature; however, there are some that make more sense than others. Currently two formulas are implimented, with plans for user-defined indices in the future:
1. (positive - negative)/(positive + negative)
2. (positive - negative)/(hemodynamic offset of the voxel)
In order to provide meaningful values, instead of using percent signal change or other measures (which might be below zero), view_sm uses the hemodynamic values calculated from FS-FAST. (Thus, as an aside, these maps can only be computed from analyses that were run with a gamma fit paramter). These values are then transformed into the rescaled values which are by default centered around 1000.
view_sm will display a selectivty map from within Matlab. There are a number of things that can be done with the selectivity map, such as view a certain slice, view a mosaic, and view the actual selectivity indices. To get more information, press ``h'' for a help window.
ARGUMENTS
REQUIRED ARGUMENTS
- -analysis analysisName
- Name of a fsfast analysis
- -positive condition number
- Condition number for the ``positive'' condition, i.e., the condition you are interested in viewing selectivity.
- -negative condition number
- Condition number for the ``negative'' condition, i.e., the condition to which you want to comapre the selectivity of the ``positive'' condition.
- -sf sessidfile
- Name of the session ID file. Note that only one session ID in the file will be used (the last one)
- -df sessdirfile
- Name of the session directory file.
OPTIONAL ARGUMENTS
- -fracmask fraction
- Specifiy a fraction of selectivity indices to show, masking all others. Note that taking a relatively high fraction, such as 0.8 or 0.9, will not clutter the map, as most selectivity indices will be clustered in the middle of the curve. The default is 0.9.
- -type selectivity index type
- Specify a type of selectivity index to compute. There are currently two indices implimented, with plans for user-defined indices in the future.
- -roimask roi_name
- Name of an ROI to use to mask the selectivity indices. If used, only those selectivity indices that are also in your ROI will be displayed. Note that your ROI directory must follow the normal conventions and must be named with the analysis given. As well, using the options -frac, -min, and -max will have no effect when using -roimask.
- -exclude
- Exclude all selectivity indices that fall outside of two standard deviations from the mean. This is only used when using an ROI to mask your selectivity indices. Be wary of using this, as it throws out data.
- -base runDirectory
- The name of a different base directory on which to overlay the selectivity map, this defaults to the first run in the bold directory or the first run in your runlist (if you have a runlist defined).
- -funcdir bold
- The name of the directory holding the functional runs, it is usually called ``bold'' and defaults to ``bold''.
- -help
- Provides complete argument information.
- -man
- Provides verbose usage information (this document).
- -debug
- Provides useful debugging information.
-
(positive - negative)/(positive + negative)
(positive - negative)/(hemodynamic offset of the voxel)
The default selectivity index formula is 1.
EXAMPLE
view_sm -analysis faces -positive 1 -negative 2 -frac 0.8 -sf sessid -df sessdir
BUGS
None known. If you find any, please send e-mail to <froi-bugs@sourceforge.net>.
AUTHOR
Nicholas Knouf, <nknouf@mit.edu>, <nknouf@mimeme.net>
COPYRIGHT & LICENSE
Copyright (c) 2003, Nicholas Knouf, MIT.
This program is free software and is governed by the terms of the Artistic License
REVISION
$Id: view_sm,v 1.6 2003/10/06 16:03:47 nknouf Exp $
SEE ALSO
make_roi, compute_roi, selxavg-sess