I'm not sure what the error is as I cannot find an actual error below. If the error is in the base creation, then send the log file for that.
On 2/8/2022 10:47 AM, Willett, Andrew Sunday wrote:
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/ //
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/awillett@bwh.harvard.edu mailto:jkim@bwh.harvard.edu* *brighamandwomens.org http://www.brighamandwomens.org//
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