This is my first time seeking support here so I apologize if I am not familiar with the community's conventions.

I am encountering errors when processing Freesurfer longitudinal stream (Freesurfer v6.0). Cross-sectional streams proceeded and completed without error, but base template creation and all following longitudinal steps failed.

I created a txt script for the base template creation: Here is a sample:
module load freesurfer
export FREESURFER_HOME=/.../.../freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

recon-all -base SA14c -tp P10 -tp P11 -tp P12 -all

This script was separate from the following step (this was a separate .txt file):
recon-all -long P12 SA14c -all -no-isrunning
recon-all -long P12 SA14c -brainstem-structures

The common error I received from the base template creation: (from the recon-all.error log==uncertain if the recon-all.log would be more illuminating for debugging)
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 user Exp $
/.../.../freesurfer/bin/recon-all
PWD /.../.../subjects/SA14c/label
CMD mri_label2label --srcsubject fsaverage --srclabel /.../.../subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject SA14c --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface

Moreover, with the base template error, it was not possible to go from there to create the individual longitudinal mri output based on the base template

I'd be really grateful for help with this debugging! Thank you.

Andrew Sunday Willett, M.S.

Department of Neurology, Division of Movement Disorders

Brigham and Women’s Hospital

awillett@bwh.harvard.edu
brighamandwomens.org

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