: Sunday, September 15, 2019 at 12:25 PM
To: FS Help
Subject: [Freesurfer] Error in running make_average_subject
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Hello Freesurfer Developers
I am trying to create an average subject for 20 subjects using the function
make_average_subject. But I keep running
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Hello Freesurfer Developers
I am trying to create an average subject for 20 subjects using the function
make_average_subject. But I keep running into a segmentation fault. I have
attached the recon-all.log file.
I found a few other posts about the
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Hello Freesurfer Developers
I am trying to create an average subject for 20 subjects using the function
make_average_subject. But I keep running into a segmentation fault. I have
attached the recon-all.log file.
I found a few other posts about the
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Hello Bruce, Doug and Emanuel,
I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded
the development version and tried that, but neither procedures fixed
the problem.
In the meantime, my father-in-law took a week and fixed the
This has been fixed in our development version. I can give you a new
script or you can try this:
cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI!
ln -s orig.mgz norm.mgz
Then re-run make_average_subject
*
On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:
>
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>
>
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Hello Bruce, Greve and Emanuel,
I have an identical problem. Have you found a solution to this issue? I'm
attaching my recon-all.log, as well, in case you need it.
Thank you!
Marta
On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo
wrote:
>
can you include the full terminal output?
On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
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Hello Bruce, thanks for your anwer. Sure. The command is
make_average_subject --out avgsubjectPRUEBAESTASI! --subjects Bartley_Recon
Baez_Recon Bonilla_Recon
The
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Hello Bruce, thanks for your anwer. Sure. The command is
*make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
Bartley_Recon Baez_Recon Bonilla_Recon*
The output is in the attached file
Thanks!
Emanuel
On Wed, Dec 12, 2018 at 7:05 PM
Hi Emanuel,
can you include the full command line and output?
cheers
Bruce
On Wed, 12 Dec 2018,
Emanuel Alvaredo wrote:
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Thanks for your answer Douglas. I replaced the make_average_surface file with
the new one but I
have the same message
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Thanks for your answer Douglas. I replaced the make_average_surface file
with the new one but I have the same message error.
ASeg Vox2RAS: ---
-1.0 0.0 0.0 128.0;
0.0 0.0 1.0 -128.0;
0.0
Sorry, the disk that held that patch failed and we did not have a backup so not
everything was restored. I just put this file there:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
Copy it to $FREESURFER_HOME/bin. Let me know how it goes
On 12/10/18
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Thanks Bruce. The following is the command.
make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
subject1 subject2 subject3
And I made a mistake in may last mail. I use the word path instead of patch
I have found this page with a
Hi Emanuel
you need to send us the full command you ran and output of it if you want
us to be able to help you
cheers
Bruce
On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
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Hello!, I am getting the following error using the command
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Hello!, I am getting the following error using the
command make_average_subject
mri/norm.mgz: could not load norm volume from (null)
I have found this page with a path for de issue
Thanks, Andrew!
On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew
wrote:
> Hi Scott,
>
> It looks like the mri_aparc2aseg binary in that patch directory was
> compiled for centos. The version at the following link was compiled on OS
> X:
Hi Scott,
It looks like the mri_aparc2aseg binary in that patch directory was compiled
for centos. The version at the following link was compiled on OS X:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg
If you download this new mri_aparc2aseg
Thanks andrew... I will try this
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: Tuesday, February 20, 2018 8:55:47 PM
To: M Janani; Freesurfer support list
Cc: Sasikala Sethu
Subject: Re: [Freesurfer] Error in running make_average_subject
Hi Janani,
W
Hey Andrew,
I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as
Janani, so I installed this patch. However, now I am getting the following
error:
#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018
/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av
\n
Hi Janani,
We have a patch for this bug here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
The second part of the readme file in that directory provides instructions for
resolving this.
best
Andrew
On February 19, 2018 at 9:40:22 AM, M Janani
Dear FreeSurfer Experts,
I’m recently getting an error in make_average_subject and can’t find
the reason.
Please see the following for the error log from recon-all.log:
mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel
mri/norm.mgz
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