Hi Montse – In case you’re still having trouble with this subject, I would check the structural segmentation (aparc+aseg from recon-all) and see if there’s anything wrong in parts of the brain that the ATR goes through. If that looks fine, then sending along the entire trac-all.log file would help with debugging.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Montserrat Domingo Ayllón <montse.domingo.ayllon@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, July 3, 2018 at 6:27 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz

External Email - Use Caution

Hi everybody!

I have an error in one of my subjects preprocessing

error opening file dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz

In the dlabel folder of this subject, the mni folder has the half of the items that the rest of subjects have (2036 vs 4568).

It is a subject with severe atrophy, therefore, I don't know if the trac-preproc has exited with errors due to this atrophy or because of other facts that I'm not able to detect.

Thank you in advance,

Montse