Functional Magnetic Resonance Imaging Lab

Faculty of Medicine and Dentistry, Palacký University
University Hospital Olomouc




Assign anatomical labels from built-in FSL atlases using atlasquery, use list of local maxima (with -l option) or zstat image (with -i option) as input. Alternatively list all anatomical structures with any thresholded activation (-a option). Run --help for more details.

Usage [OPTIONS] or atlas [OPTIONS]

-i <file> File name of the 3D volume to be clusterized.
-a <mode> List the local maxima for each anatomical structure affected. Mode 1: Cortical atlas (lateralized), Mode 2: Subcortical atlas, Mode 3: Cerebellum, Mode 4: Cortical atlas (bilateral)
-t <num> Z-threshold, set to 2.3 by default.
-l <file> Text file with the list of local maxima. Overrides -n and -a.
-c <file> Cluster mask file used to show cluster index in anatomical ROI.
-k Keep the temporary work files (including masked zstat image and cluster output)
-m <mode> Force re-creating ROI masks in /tmp/atlas_roi. Mode 1: Probabilistic mode. Mode 2: Binary mode.
-p Show progress.
-s Skip search in atlasquery.
-r Calculate and print voxels/volume ratio.
-g or --merge Merge the same structures in each upper cluster.
--help or -h Prints out this help.


Pavel Hok

Contact us

Phone: +420 588 443 418

E-mail: phlustik(at)