SYNOPSIS
make_roi -analysis analysis_name -contrast contrast_name -roi roi_name -sf sessid -df sessdir [optional arguments]
Type ``make_roi -man'' for complete documentation.
DESCRIPTION
The first step in an ROI analysis is to define the ROI. make_roi allows one to do that by thresholding a statistical map. Thresholds can be applied to either the t or significance map. As well, you can use the false discovery rate (FDR) technique to select your significance value threshold. ** insert FDR reference**
Most of the time, however, you don't want to simply include all voxels that pass a certain threshold in an ROI. Rather, you want the voxels that pass a threshold and are clustered together in a specific anatomical region. Thus, after the creation of the thresholded ROI, make_roi allows you to edit this ROI (using the same tools as in edit_roi) to select and create ROIs based on your thresholded ROI. These are the ROIs that you will most likely use in further processing.
You can get help when editing the ROI by typing ``h''. Voxels in your current ROI are in red, while voxels that are not in your current ROI but are in the thresholded ROI are in yellow.
There are many options available for make_roi that influence later processing; please read the ARGUMENTS section for more details.
ARGUMENTS
REQUIRED ARGUMENTS
- -analysis analysisName
- Name of a fsfast analysis
- -contrast contrastName
- Name of a fsfast contrast
- -roi roiName
- Name you wish to give this ROI
- -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
- -map t,sig
- Stat map for contrast contrastName to load. As of writing, the code has been tested only minimally for sig maps. Defaults to sig maps.
- -fdr value
- Instead of thresholding by a simple t or p value, threshold using False Discovery Rate (FDR). **insert ref** The default is to choose the p value that makes assumptions about the correlations of the data (that they are independent or positively dependent); these assumptions are usually valid with fMRI data. Making these assumptions gives you a more liberal p value than when making no assumptions. If you would like to make no assumptions add the -np parameter, described below. At the moment, this only applies the FDR p value to sig maps.
- -np
- When given, make no assumptions about the independence or dependence of your data. Add this paramter in addition to -fdr (described previously) if you have questions about the independence of your data.
- -threshold value
- Threshold to use when creating ROI from stat map. For both t and sig(aka, F) maps, all voxels with t (or F) values greater than this value will be included. Defaults to 2. See -map
- -base runDirectory
- When running the matlab function editOverlay, use this functional directory as the base upon which to overlay the mask. Only needs to be taken into consideration if you used different number of slices or different slice prescriptions for different runs of your scan. Defaults to the first bold directory.
- -funcDir bold
- Name of the directory holding the functional runs. Usually ``bold'', defaults to ``bold''.
- -funcStem fmc
- Name of the functional stem from which to create the base. See -base. Defaults to fmc.
- -maskdir masks
- Name of the directory under the bold directory funcDir to hold your ROIs. Defaults to analysisName_ROI, so if your analysis is called hfso, the mask directory would be called hfso_ROI and made underneath the bold directory.
- -(no)signed
-
Determines whether to take signed or unsigned values for the thresholding. If -signed, voxels will be selected that are above (below) the threshold for positive (negative) thresholds. Use -nosigned when you don't care about the sign of the stats (i.e., when you want to take all the voxels that satisfy
abs(statistics)> abs(threshold)). Defaults to -signed. See also -unsigned. - -unsigned
- Use unsigned values for thresholding. Do not use with -signed. See also -(no)signed.
- -force
- If an roi named roiName already exists, makeROI will quit. Use this option to override this behavior, but be warned that it will overwrite the existing ROI.
- -help
- Provides complete command information.
- -man
- Provides verbose usage information.
- -debug
- Provide complete debugging information.
BUGS
The code has not been extensively tested with using the -unsigned option in conjunction with -fdr.
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: make_roi,v 1.14 2003/10/06 16:03:47 nknouf Exp $
SEE ALSO
edit_roi, compute_roi