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Just bumping this inquiry. Thanks for the help.
Erin
________________________________
From: Koch, Erin M. <er...@caltech.edu>
Sent: Tuesday, February 23, 2021 9:51 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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. <er...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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:
External Email - Use Caution
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. <er...@caltech.edu><mailto:er...@caltech.edu>
Sent: Wednesday, January 27, 2021 10:04 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
It completed! Thank you the help.
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________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, January 27, 2021 10:00:54 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
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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Wednesday, January 27, 2021 7:40 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
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Koch, Erin M. <er...@caltech.edu><mailto:er...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu><mailto:dgr...@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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@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:
External Email - Use Caution
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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