At user request, a simple program to supplement 3dTrackID has been added to AFNI, in order to be able to map the tracks (*.trk file) from one space to another. The name of the program is "map_TrackID."

One can use AFNI's 3dAllineate program to calculate a map from, say, native subject space A to standard space B and save the associated transformation matrix with "-1Dmatrix_save" option. The saved matrix can then be used by map_TrackID to map the fiber bundles themselves from space A to space B. (The values of FA, MD, etc. dotted along the fibres are shifted to appropriate locations in space B by definition, since these points are the ones which *define* the bundle spatial location; they are not averaged, smoothed or otherwise re-calculated.)

NB for mapping: when you perform the tracking initially using 3dTrackID, you must use the "-rec_orig" option in order to record the "space A" origin in the header info of the track (*.trk) file. The default setting of 3dTrackID is to set the origin be (0,0,0) in the *.trk file, for the sake of visualization and rotation in TrackVis-- the value of the origin doesn't matter for aligning the tracks with underlays, but it is easier to view/rotate/manipulate the tracks *without* using the real space origin (hence the default as zeros). However, the mapping algebra requires having the real origins for both spaces A and B known, so you need to switch on the "-rec_orig" option. Additionally, when using map_TrackID, the default is *to record* the real origin in the mapped *.trk file (i.e., the tracks in B), which is useful if you will possibly map again from this space. If you want easier viewing in TrackVis, then you don't have to include the space B origin in the *.trk file header, and so may use the "-orig_zero" switch to record zeros in the origin.

As usual, any feedback/suggestions welcome.

Thanks,
pt