Re: [Freesurfer] Recon-all exiting with Errors during surface inflation

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Yes. I turned off aseg because this is NHP. In previous versions of freesurfer this was fine. Do I need to add something more my xopts file? How do I get around this problem?

Thanks,

Erin

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The problem is that it expects there to be an aseg.presurf.mgz, but you have turned the creation of it off. Because this is NHP?

On 1/15/2021 5:40 PM, Koch, Erin M. wrote:

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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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Wednesday, December 23, 2020 9:12 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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

On 12/14/2020 5:35 PM, Koch, Erin M. wrote:

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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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