Hi Michelle,
it should work like this. I don't know if it was tested with the -3T and -mprage flags. You can try to omit these flags (for testing only).
Also the SB017 has been processed cross sectionally before, right?
For debugging, you can also look at the individual steps in the base processing (like the orig.mgz, nu.mgz, norm.mgz to see if they all look OK.
Best, Martin
Am 28.09.2017 um 21:13 schrieb Michelle VanTieghem:
Hello,
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 http://casablanca.cc.columbia.edu
PROCESSOR x86_64
OS Linux
Linux casablanca.cc.columbia.edu http://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
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu mailto:mrv2115@columbia.edu
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