Hi,
I'm a fan of FATCAT, but I had a question (not directly related to FATCAT). I'm using MINIP with AND logic. My understanding is that should limit tracks to only those between ROI pairs (e.g., ROI1-ROI1). However, when I look at the *.grid file and the images that are put out by the -dump_rois (e.g., NET_000_ctx-lh-lateralorbitofrontal__ctx-lh-lateralorbitofrontal.nii.gz, I notice there are large numbers of tracks with high FA, and that they extend well beyond the ROI that is being considered (see attached figure).

The command I'm using is:

3dTrackID -mode MINIP -mini_num 5 -mask dwi_mask_ERODE2.nii.gz -netrois sel_indt_aparc+aseg_REN_gm_GMI.nii.gz -dti_in dt -prefix indipairs -logic AND -uncert dt_UNC.nii.gz -alg_Nseed_X 1 -alg_Nseed_Y 1 -alg_Nseed_Z 1 -nifti -targ_surf_stop -prefix targ_surf_stop -dump_rois BOTH

The ROIs were created from freesurfer using the guidance in the online tutorial and fit the FA map quite well. Am I misunderstanding what 3dTrackID is doing or what AND means in this context?

Thanks,
Matt



Edited 1 time(s). Last edit at 05/21/2020 12:13PM by Matthew Hoptman.