--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

--in_type fileformatname

file format name

name of the file format type of the input volume

--frame n

perform cluster analysis on 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

allow two voxels that share a corner to be considered contiguous

--mask maskstem

mask stem

filestem for mask volume used to restrict the region over which clusters will be searched. For example, this could be used to restrict the search space to only the brain (ie, exclude eyeballs). The mask must have the same dimension as the input volume.

--mask_type typename

file format for mask

--maskframe frameno

frameno to use from mask volume

use the nth frame of the mask volume as the mask, where n = 0 indicates the first frame. Default is 0.

--maskthresh maskthresh

upper threshold for mask

use only those voxels in the mask whose value exceeds the given threshold (see also --masksign and --maskinvert).

--masksign signname

sign for mask threshold

threshold the mask based on the sign of the value at each mask voxel: pos = positive, neg = negative, abs = absolute (ie, ignore sign). Default is abs. When neg is used, the a mask voxel value must be less than -maskthresh. <abs>, neg, pos

--maskinvert

invert mask

after determining which voxels are in the mask based on the threshold and sign, take only voxels that are outside of the mask

--outmask outmaskstem

stem for final binary mask

filename for the final binary mask after considering thresholding, sign, and inversion. This is mainly useful for debugging

--outmask_type fileformat

fileformat for binary mask output

--sumfile sumfilename

filename for text summary

See Description

--out outfile

filename for output volume

--out_type fileformat

fileformat for output volume

--ocn ocnfilename

output cluster number filename

filename of the output volume after clustering where the value at each voxel is the cluster number (as found in the summary file). Voxels that did not belong to a cluster have their values set to zero.

--ocn_type fileformat

fileformat for ocnfile

--label labelfile

save the nth cluster

save nth cluster (see -nlabelcluster) as a label file in the subject's anatomical space. Note: 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. Requires --nlabelcluster.

--nlabelcluster n

save nth cluster in label

--labelbase base

save all clusters

save all clusters under base-NNNN.label save each cluster in its own label file. The name of the file will be base-NNNN.label, where NNNN is the four digit, zero-padded cluster number. All clusters found will be saved.

--synth synthfunc

Legal values: uniform,loguniform,gaussian

--help

how to use this program

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description

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