Name

mri_surfcluster - This tool allows you to cluster surface data.

Synopsis

This program assigns each vertex on a cortical surface to a cluster based on the distribution of intensity values in the source file. A vertex must meet two criteria to be part of a cluster. First, its intensity must fall within a certain range (the intensity threshold criteria). Second, it must be part of a contiguous set of vertices that meet the threshold criteria and whose surface area is greater than a minimum.

There are three types of output. (1) Summary file - simple text file with a list of clusters found including maximum value, area, and talairach coordinate. (2) Filtered - identical to the input except that vertices not assigned to a cluster are set to 0. (3) Cluster number surface - this has the same format as the input and filtered output except that the value at each vertex is the cluster number assigned to it.

Arguments

--hemi hemi : lh or rh
- Specify the cortical hemisphere that the input represents. Valid values are lh and rh.

--src srcid <fmt> : source of surface values
- Input data to the clustering program. Fmt is the format specification. Currently, only paint format is supported.

--srcsubj subjid : source surface subject (can be ico)

--srcsurf surface : get coorindates from surface (white)
- Surface to use when computing the talairach coordinates. Default is white.

--srcframe frameno : 0-based frame number
- Zero-based frame number of the input file. Default is 0. For paint format, zero is the only possible value.

--thmin threshold : minimum intensity threshold
- Minimum threshold in the intensity threshold criteria. See setting the cluster intensity threshold criteria below.

--thmax threshold : maximum intensity threshold
- Maximum threshold in the intensity threshold criteria. If negative, then the maximum threshold is infinity. See setting the cluster intensity threshold criteria below.

--thsign sign : <abs>, pos, neg
- This is used to control the sign of the threshold criteria. Legal values are pos, neg, and abs. See setting the cluster intensity threshold criteria below.

--minarea area : area threshold for a cluster (mm^2)
- Minimum surface area (in mm^2) that a set of contiguous vertices must achieve in order to be considered a cluster.

--sum sumfile : text summary file
- Text file in which to store the cluster summary. See Summary File Output below.

--o outid <fmt> : input with non-clusters set to 0
- File in which to store the surface values after setting the non-cluster vertices to zero. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.

--ocn ocnid <fmt> : value is cluster number
- File in which to store the cluster number of each vertex. This can be useful for determining to which cluster a particular vertex belongs. It can be viewed as with any other surface value file. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.

--olab outlabelbase : output clusters as labels
- Save output clusters as labels. There will be a label file for each cluster. The name will be outlabelbase-XXXX.label, where XXXX is the 4-digit, zero-paded cluster number. The stat field in the label will be the value of the input statistic at that vertex.

--xfm xfmfile : talairach transform (def is talairach.xfm)
- This is a transform file that is used to compute the Talairach coordinates of a vertex for the summary file. The file must be found in subjects_dir/subjectid/transforms. The default is talairach.xfm which is based on the MNI atlas (see --fixmni).

--<no>fixmni : <do not> fix MNI talairach coordinates
- Fix (or do not fix) MNI Talairach coordinates based on Matthew Brett's
  transform. See http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html. Default is to fix. The user may elect not to fix if the xfm file is not talairach.xfm (see --xfm).

--sd subjects_dir : (default is env SUBJECTS_DIR)
- This allows the user to change the FreeSurfer subjects's directory from the command-line. If unspecified, it will be set to the environment variable SUBJECTS_DIR

# SETTING THE CLUSTER INTENSITY THRESHOLD CRITERIA

Vertices on the surface are excluded or included, in part, based on their intensity. For a vertex to be included, its value (ie, intensity) must be within a certain range (namely, between the minimum threshold, set with --thmin, and the maximum threshold, set with --thmax). While thmin and thmax must be positive values, the sign of the threshold can be set with --thsign. However, if thmax is negative, then the maximum threshold will be set to infinity. For example, if --thmin 2 --thmax 5 --thsign pos, then all vertices with values between (positive) 2 and 5 will be candidates for clustering. However, if --thsign abs is used instead, then all vertices between -2 and -5 as well as between +2 and +5 will be candidates. #

--help : answers to ALL your questions

Outputs

--sum sumfile : text summary file
- The summary file (the argument of the --sum flag) will contain a summary of the result of the clustering as well as a summary of the conditions under which the clustering was performed. It will list the clusters (1 to N) along with the maximum value found in the cluster (Max), the vertex at which this maximum value was found (Vtx Max), the surface area of the cluster (Size), and the Talaiarach coordinates of the maximum (based on talairach.xfm).

--o outid <fmt> : input with non-clusters set to 0

--ocn ocnid <fmt> : value is cluster number

--olab labelbase : output clusters as labels

Bugs

Currently only supports paint (or w) format for input and output.