Program: 3dclust Author: RW Cox et al Date: 21 Jul 2005
3dclust - performs simple-minded cluster detection in 3D datasets
This program can be used to find clusters of ‘active’ voxels and print out a report about them.
- ‘Active’ refers to nonzero voxels that survive the threshold
that you (the user) have specified
Clusters are defined by a connectivity radius parameter ‘rmm’
- Note: by default, this program clusters on the absolute values
- of the voxels
3dclust -1clip 0.3 5 2000 func+orig’[1]’ 3dclust -1noneg -1thresh 0.3 5 2000 func+orig’[1]’ 3dclust -1noneg -1thresh 0.3 5 2000 func+orig’[1]’ func+orig’[3]
3dclust -noabs -1clip 0.5 -dxyz=1 1 10 func+orig’[1]’ 3dclust -noabs -1clip 0.5 5 700 func+orig’[1]’
3dclust -noabs -2clip 0 999 -dxyz=1 1 10 func+orig’[1]’
3dclust -1clip 0.3 5 3000 func+orig’[1]’ 3dclust -quiet -1clip 0.3 5 3000 func+orig’[1]’ 3dclust -summarize -quiet -1clip 0.3 5 3000 func+orig’[1]’ 3dclust -1Dformat -1clip 0.3 5 3000 func+orig’[1]’ > out.1D
- rmm : cluster connection radius (in millimeters).
All nonzero voxels closer than rmm millimeters (center-to-center distance) to the given voxel are included in the cluster.
- If rmm = 0, then clusters are defined by nearest- neighbor connectivity
- vmul : minimum cluster volume (micro-liters)
- i.e., determines the size of the volume cluster.
If vmul = 0, then all clusters are kept.
- If vmul < 0, then the absolute vmul is the minimum
number of voxels allowed in a cluster.
- dset : input dataset (more than one allowed, but only the
- first sub-brick of the dataset)
The results are sent to standard output (i.e., the screen)
Editing options are as in 3dmerge (see 3dmerge -help) (including -1thresh, -1dindex, -1tindex, -dxyz=1 options)
-noabs | => Use the signed voxel intensities (not the absolute value) for calculation of the mean and Standard Error of the Mean (SEM) |
-summarize | => Write out only the total nonzero voxel count and volume for each dataset |
-nosum | => Suppress printout of the totals |
-verb | => Print out a progress report (to stderr) as the computations proceed |
-1Dformat | => Write output in 1D format (now default). You can redirect the output to a .1D file and use the file as input to whereami for obtaining Atlas-based information on cluster locations. See whereami -help for more info. |
-no_1Dformat=> Do not write output in 1D format.
-quiet | => Suppress all non-essential output |
-mni |
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-isovalue |
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-isomerge |
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-inmask |
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input, but with all voxels not in a cluster set to zero; the new dataset’s prefix is ‘ppp’
first input dataset.
that the largest cluster is labeled ‘1’, the next largest ‘2’ and so forth. Should be the same as ‘3dmerge -1clust_order’ or Clusterize ‘SaveMsk’.
E.g., 3dclust -1clip 0.3 5 3000 func+orig’[1]’
The above command tells 3dclust to find potential cluster volumes for dataset func+orig, sub-brick #1, where the threshold has been set to 0.3 (i.e., ignore voxels with an activation threshold of >0.3 or <-0.3. Voxels must be no more than 5 mm apart, and the cluster volume must be at least 3000 micro-liters in size.
- Volume : Volume that makes up the cluster, in microliters (mm^3)
- (or the number of voxels, if -dxyz=1 is given)
- CM RL : Center of mass (CM) for the cluster in the Right-Left
- direction (i.e., the coordinates for the CM)
- CM AP : Center of mass for the cluster in the
- Anterior-Posterior direction
- CM IS : Center of mass for the cluster in the
- Inferior-Superior direction
- minRL, maxRL : Bounding box for the cluster, min and max
- coordinates in the Right-Left direction
- minAP, maxAP : Min and max coordinates in the Anterior-Posterior
- direction of the volume cluster
- minIS, max IS: Min and max coordinates in the Inferior-Superior
- direction of the volume cluster
Mean : Mean value for the volume cluster
SEM : Standard Error of the Mean for the volume cluster
Max Int : Maximum Intensity value for the volume cluster
- MI RL : Coordinate of the Maximum Intensity value in the
- Right-Left direction of the volume cluster
- MI AP : Coordinate of the Maximum Intensity value in the
- Anterior-Posterior direction of the volume cluster
- MI IS : Coordinate of the Maximum Intensity value in the
- Inferior-Superior direction of the volume cluster
Nota Bene:
- The program does not work on complex- or rgb-valued datasets!
- Using the -1noneg option is strongly recommended!
- 3D+time datasets are allowed, but only if you use the
-1tindex and -1dindex options.
- Bucket datasets are allowed, but you will almost certainly want to use the -1tindex and -1dindex options with these.
- SEM values are not realistic for interpolated data sets! A ROUGH correction is to multiply the SEM of the interpolated data set by the square root of the number of interpolated voxels per original voxel.
- If you use -dxyz=1, then rmm should be given in terms of voxel edges (not mm) and vmul should be given in terms of voxel counts (not microliters). Thus, to connect to only 3D nearest neighbors and keep clusters of 10 voxels or more, use something like ‘3dclust -dxyz=1 1.01 10 dset+orig’. In the report, ‘Volume’ will be voxel count, but the rest of the coordinate dependent information will be in actual xyz millimeters.
- The default coordinate output order is DICOM. If you prefer the SPM coordinate order, use the option ‘-orient LPI’ or set the environment variable AFNI_ORIENT to ‘LPI’. For more information, see file README.environment.
++ Compile date = Dec 16 2015