The lab I work in recently upgrade to freesurfer-linux-centos7x_86_64-7.1.1 from freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0, and I am trying to use a series of shell scripts (that call freesurfer) which we successfully used to run to create flatmaps
for non-human primate sessions. I am stuck when using recon-all to inflate the surface. Specifically, I am running the command:
"recon-all -autorecon2-wm \
-subjid ${tmp_subj} ${corpcal_coord_string} ${pons_coord_string}\
-noaseg \
-mprage \
-xopts-use\
-debug\"
This step runs for quite some time, seemingly making progress and then "Exits with errors" . In the terminal the error message that I can see is: "ERROR: need seg for ripping". This is followed by: "recon-all - s SUBJECTNAME exited with ERRORS." (Screen
shot of this error is attached). I will also attach the recon-all.log.
This issue does not seem to be a problem of quality of skull stripping or white matter segmentation, as the session can be completed with the older version of freesurfer, adn I get the same error with different sessions and subjects. Can you please shed
some light on this? The machine I am using is running Linux 3.10.0-1127.18.2.e17.x86_64 .
As an aside - Do you have any references or outline for flat map creation (specifically for non-human primates) with the newer versions of Free surfer? It is possible adapting our old pipeline is not ideal / there are more efficient or "better" ways to
do this now.
Thank you for your help.
Best,
Erin