The AFNI-FATCAT (Taylor & Saad, 2013) set of programs has been updated to v2.1.

In the process of updating from FATCAT v1.1, several small and a few large features have changed, including:

• the inclusion of multi-directional tracking for HARDI-modeled data (3dTrackID);
• improvements in SUMA-visualization capability (so one should make sure to have an uptodate version of SUMA, as well);
• multi-network naming formats to match brik numbers consistently (3dTrackID, 3dNetCorr);
• ability to load multiple scalar data sets into tracking for more simple statistics in WM-ROIs;
• more labelling in output GRID and NETCC files (3dDWUncert and 3dNetCorr;
• for some longer programs, outputting progress percentages (3dTrackID and 3dDWUncert);
• and, most readily noticeable, a number of changes to the naming/commandline/option capability of tracking-- hopefully there's much less potential for confusion about inputs (the various MODES have been formalized), and the user has more flexibility in controlling runtime algorithm options (3dTrackID).

The demo set has been updated in large part to include examples of all forms of tracking (deterministic, mini-probabilistic and probabilistic), and both DTI and HARDI/multi-directional. Also, visualization examples show some of the increased SUMA capabilities, with more help tools/descriptions in the works for that. To download, install, and uncompress the Demo file in one fell swoop, type the following in a terminal commandline:
$ @Install_FATCAT_Demo
There is a README.txt file there with a guide to each script and the data sets therein. Each script also has a number of comments for guidance.

The new demo will require that you update the afni binaries:
$ @update.afni.binaries -d

A special note about tractography/name changes: basically, the naming conventions for different modes of tractography were deemed to be quite awkward, by both the author and other users of the program. Gone is the old program name '3dProbTrackID', with its assortment of switches/options for deterministic switches and things. Now, main running of tractography will be run through the following name and mode selection:
$ 3dTrackID -mode { DET |MINIP | PROB } ...
whereby one selects a respective mode of deterministic, mini-probabilistic or full-probabilistic tracking. One also then chooses options for loading either DTI or HARDI data, and then there are a number of algorithmic variables the user can control. The list of options associated with each mode is given in a hopefully-clear table in the 3dTrackID help file.

(It was deemed that old naming conventions were too tied up, and if there were to be some updates, then everything had better be migrated at once. If anyone has any questions about switching their own scripts/commands affected by the ->3dTrackID move, please send them early and often.)


--pt