Hi 

Thanks for your help.  Indeed the list of commands you sent worked, so I added the line you recommended to my xopts.  This gets me beyond my previous exit point, but now recon-all is exiting with a new error.  I will attach my recon-all log and terminal error.   It seems recon-all is trying to load an aseg file; however, I include in my call -noaseg (and I tried adding -nosubcortseg).

Please let me know if you need anything else.  

Erin 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, December 23, 2020 9:12 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

There have been some changes that are breaking your stream. Try this

cd /mnt/data2/data/erink/cooked/2019/190124Jamie2/mri
setenv SUBJECTS_DIR /mnt/data0/home/erink/subjects
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion

If that works, then add this to your xopts file
 WhitePreAparc --no-rip-midline --no-rip-bg --no-rip-wmsa --no-rip-freeze --no-rip-lesion

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Hi all, 

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 

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