It should not need it for the inflation. You can try adding -no-cortex-label and see how far you get
On 1/27/2021 12:39 PM, Koch, Erin M. wrote:
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Thanks for the info. Is it possible to put in a "fake" aseg.presurf.mgz file? Do you think this is a possible work around, or is the inflation for flat map generation somehow reliant on this file now?
Erin
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Wednesday, January 27, 2021 7:40 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation It needs to be there. Sorry, I rewrote parts of the stream for v7 and did not consider the impact on NHP streams (since they are not part of our package). You might have to use older versions of FS to make this work.
On 1/26/2021 11:10 PM, Koch, Erin M. wrote:
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Or, are you saying that I do not need to turn it off for NHP?
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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Koch, Erin M. erink@caltech.edu mailto:erink@caltech.edu *Sent:* Monday, January 25, 2021 10:47:34 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* 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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*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, January 25, 2021 8:01:12 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu *Sent:* Wednesday, December 23, 2020 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto: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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