Hi Ping - It looks like the path initialization may have failed. The algorithm needs an initial guess for the path and iterates from there. This initial guess is chosen based on the tracts in the atlas and if your subject is not perfectly aligned with the atlas this initial guess might end up going off the white matter for example. Does the blue line in your snapshot look like it may not coincide well with you subject's CST, going off the white matter close to the end, etc?
a.y On Thu, 22 Sep 2011, Ping-Hong Yeh wrote: > Hello, > > The segmented left CST tracts of one of our 3T data was not > satisfactory, which has only few voxels with 1000 gray values (see > attached snapshot pictures for "trac-all" and "cst_prob"). The > manually tracking using deterministic tractography seems OK (see > cst_stremline). Any suggestions on which step may go wrong in > trac-all? > > Thank you, > > Ping > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
