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Just bumping this inquiry. Thanks for the help.
Erin
From: Koch, Erin M.
Sent: Tuesday, February 23, 2021 9:51 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exiting with Errors during
.
Sent: Wednesday, February 17, 2021 11:14 AM
To: 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
nd to create these files?
thanks,
Erin
*From:* Koch, Erin M.
*Sent:* Wednesday, January 27, 2021 10:04 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] Recon-all exiting with Errors during
surface inflation
It completed! Thank you the help.
Get Outloo
PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
It completed! Thank you the help.
Get Outlook for
iOS<https://secure-web.cisco.com/1gwWbpdPd_e4hzx4PaKLpKZ-dn71TvezCR90YEOyHZ0I-QlRoQ9
:00:54 AM
To: 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
2021 7:40 AM
*To:* 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 mig
_
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Wednesday, January 27, 2021 7:40 AM
To: 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 str
Monday, January 25, 2021 10:47:34 PM
*To:* Freesurfer support list
*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
Monday, January 25, 2021 10:47:34 PM
To: Freesurfer support list
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 som
.ms%2Fo0ukef>
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, January 25, 2021 8:01:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Recon-all exiting with Errors during surface inflation
The problem i
@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
: 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
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
Hi Julia
I don't see any error messages. If you upload the dataset we'll take a
look. Make sure you have enough ram in the machine (>2G) and free disk
space.
cheers
Bruce
On Tue, 15 May 2012, Richter, Julia wrote:
> Dear FreeSurfer experts,
>
> I am trying to recon-all T1 images with the com
Dear FreeSurfer experts,
I am trying to recon-all T1 images with the command recon-all -s
-i /path/to/subject/directory/subject.nii.gz. This command used to work with
several images, but one of my images is always exiting with errrors, in my
opinion without a reason. Any suggestions what is go
Hello, I am trying to run recon-all but it seems to have some problems
during nu_correct. I am using the command recon-all -subjid SM2C1tal
-stage1, my subjectsdir is /space/troy/1/users/FREESURFER, and I am
getting the error, Can't locate MNI/Startup.pm in @INC. then it says all
the stuff @INC
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