Hi Ansgar - From looking at your data, the reconstruction of the ccg failed b/c it goes erroneously into an area superior of the cingulum. You can see this clearly by looking at the slice view of the cingulum in freeview (the isosurfaces in the 3D view don't always tell the whole story).

It's possible that this is due to failure in the initialization of the tractography algorithm. An initial guess for each path is chosen from the set of subjects included in the atlas and sometimes it doesn't align well with an individual subject. You can look at the histogram of the paths from the atlas subjects at: dlabel/mni/lh.ccg_PP_avg33_mni_flt_histo_str.nii.gz And the one path that was chosen form that set to initialize tractography in your subject at: dlabel/mni/lh.ccg_PP_avg33_mni_flt_cpts_5.nii.gz

In this case you'll see that the latter is at the superior border of the cingulum and not in the middle of the cingulum. I'd check other cases where you had the same problem to see if this also occurs.

To change the initialization, you can set reinit = 1 in your configuration file and rerun the -prior and -path steps, only for the pathway and subject that failed. Every time you rerun with reinit = 1, it will pick an initialization that it hasn't picked before.

Hope this helps, a.y

Dear All, Please ignore my earlier incomplete message with the same title! We are using the ADNI Acc 3D FSPGR for structurals and a 30 directional (5 B0s) dual-spin repeat sequence for DTI (on a 3T GE 750 discovery) which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely "crippled" tracts which, however, is not consistent with their FA maps. The crippling is most visible when comparing left vs right cingulate gyri. In some cases either the left or right side is almost completely gone. Has anyone else experienced similar issues and found a remedy? Thanks a lot, Ansgar _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer