I am running the -base processing so that I can create a subject-specific template for the -long processing. I have some subjects with only 1 timepoint. According to the website, all versions 5.2 and higher can handle 1 time point when making the base. I am using freesurfer 5.3. 

However, when I run the -base commands, it's working fine for subjects with 2-3 scans but fails  mid way through processing for subjects with only 1 scan. I cannot determine why this is happening,  and it happens at *different stages* of processing. (e.g. fix topology or CA Reg) 

 the recon-all.error log does not provide useful information. Is there an extra flag that i am missing: 

Here is an example command:

recon-all -base SB017templatebaseline -tp SB017 -all -3T -mprage

Here is a recon-all.error log:

------------------------------

SUBJECT SB014templatebaseline

DATE Thu Sep 28 15:00:02 EDT 2017

USER mrv2115

HOST casablanca.cc.columbia.edu

PROCESSOR x86_64

OS Linux

Linux casablanca.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux

$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $

/vega/psych/app/freesurfer/bin/recon-all

PWD /vega/psych/users/mrv2115/fsdata/processed/CLEAN/SB014templatebaseline/scripts

CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 SB014templatebaseline rh

--