Name

mri_volcluster - find clusters in volume

Synopsis

mri_volcluster --in inputstem --minsize minclustervolume --thmin minthresh --reg register.dat

Arguments

Required Flagged Arguments

--in inputstem

input stem for volume to be clustered

--minsize minclustervolume

minimum volume of cluster in mm 3

minimum volume (in mm 3) of contiguous voxels that meet the threshold criteria needed to become a cluster. See also --minsizevox

--thmin minthresh

minimum voxel intensity for cluster voxels

voxel values must exceed this amount to be considered as a candidate for a cluster

--reg register.dat

registration file

registration file created by either tkregister or tkmedit. Note: the subject listed in the registration file must have an entry under $SUBJECTS_DIR

Optional Flagged Arguments

--in_type fileformatname

file format name

name of the file format type of the input volume

--frame frameno

perform the cluster analysis on the nth frame

The first frame corresponds to n=0

--thmax maxthresh

maximum voxel intensity for cluster

voxel values must exceed this amount to be considered as a candidate for a cluster Default: infinity

--sign signname

Legal values: <abs>, neg, pos

the value of a voxel must be this sign to be considered as a candidate for a cluster. pos = positive, neg = negative, abs = absolute (ie, ignore sign). Default is abs. When neg is used, the interpretation of minthreshold and maxthreshold are reversed

--minsizevox number

minimum volume (voxels)

minimum number of contiguous voxels that meet the threshold criteria needed to become a cluster. See also --minsize

--mindistance distance

distance threshold

minimum distance (in mm) that the peaks of two clusters must be separated in order for them to be considered two distinct clusters. If two clusters are closer than this amount, the cluster with the lower peak is eliminated.

|| --allowdiag : define contiguity to include diagonal || --mask mask volid (same dim as input) || --mask_type file format || --maskframe frameno <0> || --maskthresh upper threshold || --masksign <abs>, neg, pos || --maskinvert || --outmask final binary mask || --outmask_type file format || --sum file : text summary file || --out outupt volid || --out_type file format || --ocn output cluster number volid || --ocn_type file format || --label label file || --nlabelcluster n : save nth cluster in label || --labelbase base : save all clusters under base-NNNN.label || --synth synthfunc (uniform,loguniform,gaussian) || --help : how to use this program

Outputs

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description

Description

mri_volcluster will find clusters in a volume. A cluster is a set of contiguous voxels which meet a threshold criteria. The set may also have to reach a certain minimum number of voxels to be considered a cluster. The results can be saved in four ways: (1) a text summary file, (2) a new volume which is same as the input volume but with all the voxels that do not belong to a cluster set to zero, (3) a volume with each voxel's value equal to the cluster number in the summary file to which the voxel belongs, and (4) one cluster can be saved as a label file. The search space within the volume can be restricted to be within a mask. Two voxels are considered contiguous if they share a common row, column, or slice (except for --allowdiag).

Examples

Example 1

mri_volcluster ??

Description

Example 2

mri_volcluster ??

Description

Bugs

When specifying a label file, make sure that the label file includes a forward slash (/) or the label will be saved into the subjects anatomical direcotry. For example: ./mylabel.label

See Also

["othercommand1"], ["othercommand2"]

Links

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

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

Author/s

DougGreve