Hi Linnea Marie – You’re right in your assessment. Are you using 6.0? You can reinitialize those bad cases, by adding “set reinit = 1” in your config file and changing the path list and subject list to specify only the tract and subjects that you want. Then rerun trac-all --prior and trac-all —path for those cases.

Best,

a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Linnea Marie Dramdal Borg <lmborg@stud.ntnu.no>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, October 6, 2017 at 6:13 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA qc: forceps minor and major

Hi, 


We have run into some issues with our forceps major and forceps minor tractographies. I have attached examples: In "fminor_bro_139.png", there is a "bridge" in forceps minor in the space between the hemispheres. We've also come across other cases of bridging in forceps minor, with somewhat unusual voxel intensity distribution, such as in "fminor_onestripe_otherwOK.png" and" fminor_litenbro_OKornot_210.png".   Also, "fmajor_132_toolateral.png", fmajor brances out in the left hemisphere (right in the picture).  All of these cases seem pretty bad to us. Do you agree?


In contrast, "fminor_allslicesOKbutone_158.png" looks fine, but there is one slice where it branches out to some extent. Are we correct in assuming this won't affect the results too much, or is there something we can/should do about this? 



Thank you, 


Linnea Marie