Index

Contents

  1. Name
  2. Synopsis
  3. Arguments
    1. Define the anatomical label
    2. Define the functional constraint
  4. Description
    1. Specifying the Anatomical Constraints
    2. Specifying the Functional Constraint
  5. Examples
    1. Example 1
  6. Bugs
  7. See Also
  8. Links
  9. Reporting Bugs

Name

funcroi-config

Synopsis

Arguments

-roi roiconfig

Name of the configuration file. Eg, left-hippocampus. Later, data files will be named based on this file name. If ".roicfg" is the extension, the name of the roi will have this extension removed.

-force

Delete any existing roiconfig files

Define the anatomical label

-label labelname

-annot annotname labelname

(hemi.annotname.annot)

-seg segvol segid

-fillthresh fillthresh

Define the functional constraint

-analysis analysisname

Name of analysis configuration

-contrast contrastname

-thresh threshhold

-sign sign

abs, pos, neg

-map map

Default is sig

-frame frameno

Frame within contrast sig (default is 0)

Description

Configures a region-of-interest (ROI) based on subject-specific anatomical and, possibly, functional definitions. This does not perform the analysis; it only configures the parameters needed to define the ROI for later analysis with funcroi-sess and/or funcroi-table-sess. The output is a simple text file (the configuration).

Specifying the Anatomical Constraints

There are four possible ways to define the anatomical part of the ROI, two for surface-based analyses and two for volume based:

  1. Surface label (-label)
  2. Surface annotation (-annot)
  3. Volume label (also -label)
  4. Volume segmentation (-seg)

You must specify an analysis to use. The analysis (-analysis) space must match that of the anatomical ROI space. Ie, if the anatomical ROI is defined by a surface annotation, then the analysis must be a surface-based analysis. If the anatomical ROI is defined in the volume using a segmentation or a volume label, then the analysis must be volume-based (ie, mni305 or native).

The volume methods can be modified with the -fillthresh option, which is a number between 0 (the default) and 1. When mapping an anatomical volume ROI into the functional analysis space, there will be a difference in resolution (1mm for the anatomical and maybe 2mm for the analysis). This means that each analysis voxel may only be partially filled. The fill threshold indicates how full the analysis voxel must be in order for it to be considered part of the ROI. Eg, "-fillthresh 0.5" indicates that the analysis voxel must be at least half full. This will only make a difference on the edges of structures.

Note that these are subject-specific anatmomical ROIs even when you use fsaverage or mni305 as an analysis space because the subject-specific ROIs are mapped into these spaces (and so stay subject-specific).

Specifying the Functional Constraint

The functional constraint is specified through a contrast (-contrast) of the given analysis along with a threshhold (-thresh) and a sign (-sign). You can also change the map (default is sig) and the frame in the map (default is 0). The functional map is thresholed at the given level with the given sign to create a binary mask. This mask is then intersected with the anatmomical constraint to create the final ROI.

Examples

Example 1

Bugs

None

See Also

othercommand1, othercommand2

Links

FsFast

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>