Hi Tamara, 

 this should finish the longitudinal recon-all. It picks it up from where you edited and completes the rest. It needs to know about the name of the time point and the name of the base to access files from there (e.g. to map initial surfaces from base ect).

Best, Martin

Hello,

I have made edits to aseg files in the longitudinal outputs (participantID.long.participantID-temp). I am beginning the reconstruction phase and as suggested by a response to an earlier post I am running: recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1 is cross-sectional output and template ID is the template of the participant. 

My questions are:

1)  Does the script essentially take the edits I made in the aseg longitudinal outputs and reconstructs the longitudinal files using the cross and template files?

2) Does this script begin running recon-all during recon-all2, after the aseg files are suppose to be created?

Thank you,

Tamara

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu