External Email - Use Caution
As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and
binary backwards compatibility cannot be expected to work indefinitely going
forwards to newer versions of the OS. I ran a simple mri_surf2surf
command from 5.1.0 on CentOS7
] Segmentation fault (core dumped)
External Email - Use Caution
Greetings FS experts:
We are trying to run recon-all -s -qcache on a handful of brains processed in
freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for our
purpose.)
The error is below:
[cid:image00
External Email - Use Caution
Greetings FS experts:
We are trying to run recon-all -s -qcache on a handful of brains processed
in freesurfer v5.1.0. (it's an old dataset...5.1 makes the most sense for
our purpose.)
The error is below:
[image: image.png]
---
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Hello Yuhui,
Did you try something like the following (from
https://secure-web.cisco.com/1hub7Psr57JCR6YgoGWEJLmEuz6voF9O_4wwW1Ngq-Krek8hQagKNFY9pH9jg_UzrEMFBjBl1Lo36JvBnp02E7HopuMgcNTaG0pTRx-2PR61unk8dCsv-4Gp50vSlBbeEJzjsRZGWS1jqAp0pVmSzDy9Ob23Rg1PB3s
External Email - Use Caution
Hello,
As a beginner, I am trying to run freeview -v using tutorial_data by the code
below.
freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_o
N Greve
>
> *Sent:* Monday, December 18, 2017 5:09:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Segmentation fault (core dumped)
>
> We need more details. Try looking at this web site
>
>
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
o:* Freesurfer support list [freesurfer@nmr.mgh.harvard.edu]
> *Cc:* Jacobs, Heidi Irma Louisa; Vannini, Patrizia,Ph.D.
> *Subject:* [Freesurfer] Segmentation fault (core dumped)
>
> Dear FreeSurfer experts,
>
>
> I am unable to run the qcache procedure and was wondering if a
freesurfer@nmr.mgh.harvard.edu]
Cc: Jacobs, Heidi Irma Louisa; Vannini, Patrizia,Ph.D.
Subject: [Freesurfer] Segmentation fault (core dumped)
Dear FreeSurfer experts,
I am unable to run the qcache procedure and was wondering if anybody could help
me find what is going on.
I've tried running qcac
x range to be [126, 130] in xformed coordinates
> best xformed slice 128
> cc center is found at 128 117 99
> eigenvectors:
> 0.00099 0.00201 1.0;
> -0.30008 -0.95391 0.00221;
> 0.95391 -0.30008 -0.00034;
> Segmentation fault (core dumped)
> Linux neuroimaging01 4.8.0-52-g
matic section. I will report,
if the issue appears there, too.
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr
Von: "Jens Offenbach"
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I
An: freesurfer@nmr.mgh.harvard.edu
Cc: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects
from OASIS-Brains.
I will retry the run.
This is the last log entry:
mri_cc -aseg
: Freitag, 26. Mai 2017 um 15:52 Uhr
Von: "Devin Sodums"
An: "Freesurfer support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
Sure thing, I’ll send it in a few.
Thanks,
Devin
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr
Sure thing, I'll send it in a few.
Thanks,
Devin
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Friday, May 26, 2017 9:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation fault (core d
No idea. Can you upload the subject so I can take a closer look?
https://gate.nmr.mgh.harvard.edu/filedrop2
On 5/26/17 9:35 AM, Devin Sodums wrote:
Hello FreeSurfer developers,
I’m attempting to run recon-all on a T1 image and keep getting the
same error message:
Segmentation fault (core d
It did not find any voxels in the ROI. This can happen for several
reasons. First, check your registratoin (tkregister-sess). Second, it
can happen because the size of the ROI is too small and does not occupy
enough space in a voxel. Try changing the -fillthresh to something
smaller than the de
Hello FS experts,
I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat
file for further analysis. I used the same steps to calculate FC for 40
subjects, all steps run fine with 38 subjects but for 2 subjects I am
getting an error: Segmentation fault: Core dumped.
I checked the
what server did you upload it to? What is the name of the file? Make
sure to include the entire output folder, not just the input files
On 12/21/2015 03:33 PM, Fengji Geng wrote:
> Hi Bruce,
>
> I have uploaded all the data to the server. The command that I run is
> 'recon-all -all -s $s -hippoc
Hi Bruce,
I have uploaded all the data to the server. The command that I run is
'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.
It would be great if you could keep us updated on how the fixing is going.
Thanks!
--
Martina,
Can you send me the recon-all.log file?
Nick
On Tue, 2013-05-07 at 17:38 +0200, martina.andell...@fastwebnet.it
wrote:
> Hi Freesurfer experts,
> I've got Ubuntu version 13.04 installed on my computer, and after I saw the
> post
> : "http://www.mail-archive.com/freesurfer@nmr.mgh.harv
Hi Freesurfer experts,
I've got Ubuntu version 13.04 installed on my computer, and after I saw the post
: "http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28267.html"; I d
ecide to install the BETA version freesurfer-Linux-centos6_x86_64-stable-pub-v5.
3.0-BETA.tar.gz as adviced.
I st
Dear Mr or Ms,
My computer was installed with Freesurfer v4.0.3,centos4,
To make an average surface,I launch "make_average_subject" command,
I come across an error :
Processing subject 25/52 sh45 ...
Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
Segmentation fault (core dumped)
Dear Mr or Ms,
My computer was installed with Freesurfer v4.0.3,centos4,
To make an average surface,I launch "make_average_subject" command,
I come across an error :
Processing subject 25/52 sh45 ...
Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg
Segmentation fault (core dumped)
Renat,
You should try running the centos4 build of freesurfer on Fedora Core 3.
The wiki site incorrectly stated to use the rh9 build with fc3, but
after speaking with our sysadmin, apparently Fedora Core 3 (fc3) is
closer in likeness to Centos4, so you may want to give the centos4 build
a try.
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