External Email - Use Caution
Just want to bump this message. Please let me know if you have any suggestions.
Best,
Erin
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Koch, Erin M.
<er...@caltech.edu>
Sent: Friday, January 15, 2021 2:40 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
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
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.
<dgr...@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:
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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