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Is there anyway to get the lh.white and rh.white with noaseg?  Or is there a file in the attachment of the previous email that is a stand in for those missing files?

Thanks for your help. 
Erin 
From: Koch, Erin M. <erink@caltech.edu>
Sent: Wednesday, February 17, 2021 11:14 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
 
I am attaching a screen shot of the files in my subjects surf subfolder.  Note in the image you only see the lh.*** surfaces.  All correspoinding rh.*** files are there as well. 

Thanks!  
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, February 12, 2021 6:54 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
 
What surfaces are there?

On 2/11/2021 4:35 PM, Koch, Erin M. wrote:

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Hi Douglas, 

I am sorry I have to bug you once more.  While the inflation step completed with the suggested flag, as did the flattening step (for creating a flat map), when I went to register a functional scan to the inflated and flat map  the command:

mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi lh —out 'PVal_lh') 
mri_vol2surf —src 'PVal_resliced' —srcreg reg.dat —projfrac 0.5 —interp nearest —hemi rh —out 'PVal_rh')

failed because the recon-all did not create a few files including: lh.white, and rh.white 

Is this due to the flags and expert options that were needed to complete the inflation?
Can I run a separate command to create these files? 

thanks, 

Erin 
From: Koch, Erin M. <erink@caltech.edu>
Sent: Wednesday, January 27, 2021 10:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
 
It completed!  Thank you the help. 

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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 10:00:54 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
 
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 <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Koch, Erin M. <erink@caltech.edu>
Sent: Monday, January 25, 2021 10:47:34 PM
To: Freesurfer support list <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 <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, January 25, 2021 8:01:12 PM
To: freesurfer@nmr.mgh.harvard.edu <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 <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

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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