Hi Nick,
Thank you so much for your response. Turns out that the XQuartz had updated to
2.7.6, I've reinstalled 2.7.5 and it is working!
Finally I can finish this study!
Best wishes,
Gill
_
Gillian Cooke, Ph.D.
Postdoctoral Research Associate
Lifelong Brain & Cognition Lab
B
support list
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Seg fault
>>
>> It is happening with all subjects that I've loaded this week, but this
>> is my second pass through checks on this data - so all have previously
>> loaded successf
Hi,
So I've now tried several subjects on my own computer and they all gave me this
fault.
I then tried several on another and it worked.
If I didn't update my OS version or my freesurfer version, is there another
software update that could give me this fault?
Many thanks,
Gill
On May 30, 201
It is happening with all subjects that I've loaded this week, but this is my
second pass through checks on this data - so all have previously loaded
successfully.
On May 30, 2014, at 11:24 AM, Douglas N Greve wrote:
>
> It might be the data you are trying to load in. Does it happen with
> oth
It might be the data you are trying to load in. Does it happen with
other subjects or volumes?
On 05/30/2014 12:17 PM, Cooke, Gillian wrote:
> Thanks for the quick responses.
> I'm using version 10.7.5 - I purposely haven't updated this as we've been
> analysing a large set of intervention data
Thanks for the quick responses.
I'm using version 10.7.5 - I purposely haven't updated this as we've been
analysing a large set of intervention data.
I'm also using freesurfer-Darwin-lion-stable-pub-v5.3.0 - again we've been
consistent with this and have run everything in this version.
I'm still
Hi Gillian
what changed? Did you upgrade a video driver? Use a new machine? Update
the operating system? Run out of disk space? Something is different
Bruce
On
Fri, 30 May 2014, Cooke, Gillian wrote:
Hi,
I've been working with Freesurfer for years and have suddenly been getting
this fa
Hello Gill,
Can you provide me with the version number of OSX you are using (Apple
-> About This Mac), and the contents of your
/Applications/freesurfer/build-stamp.txt file?
Also, did you recently do an upgrade of your system?
-Zeke
On 05/30/2014 12:00 PM, Cooke, Gillian wrote:
> Hi,
>
> I'v
Hi,
I've been working with Freesurfer for years and have suddenly been getting this
fault:
tkmedit started: Fri May 30 10:08:23 2014
/Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz
-aux T1.mgz -surfs
$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: sta
Hmmm, I can't replicate this error. This is 5.3 I assume?
doug
On 11/12/2013 06:02 PM, Michael Waskom wrote:
> sorry, unclear why the original email wasn't included in the reply.
> copied here:
>
>
> I'm running into a strange seg fault when trying to use mri_segstats
> (it's actually ocurrin
I am a bit stumped. Can you check that cache.th20.pos.sig.ocn.mgh and
concat_output.nii.gz? I'm sure they most be. If so, send both to me on
our file drop.
doug
On 11/04/2013 07:00 PM, Michael Waskom wrote:
> Hi Doug,
>
> I'm running into a strange seg fault when trying to use mri_segstats
Hi Doug,
I'm running into a strange seg fault when trying to use mri_segstats (it's
actually ocurring within mri_glmfit-sim, but I can reproduce it manually)
This is the line that fails (stripping the leading paths for readability):
mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0 --i
I mean multiple subjects simultaneously on the same machine
On Mon, 3 Aug 2009, Nathan Dankner wrote:
Do you mean running multiple subjects simultaneously or more than one recon
on an individual subject? In either case, the answer is yes. I could try
running them individually to see if the pr
Do you mean running multiple subjects simultaneously or more than one recon
on an individual subject? In either case, the answer is yes. I could try
running them individually to see if the problem persists.
On 8/3/09 3:42 PM, "Bruce Fischl" wrote:
> yes, I just saw that. I thought it only hap
yes, I just saw that. I thought it only happened when the machine ran out
of memory. Are you running more than 1 recon at a time?
On Mon, 3 Aug 2009,
Nathan Dankner wrote:
I have 4 gigs of ram on here. This is the response that I got from Nick
Schmansky:
This is a known and long-standing pro
I have 4 gigs of ram on here. This is the response that I got from Nick
Schmansky:
This is a known and long-standing problem with mris_volmask. The fault
occurs deep within a library, VTK, of which we make use (null pointer in
vtkDataArrayTemplate::GetTuple). We're trying to find a fix or
worka
looks like it's failing in mris_volmask. How much RAM do you have on your
machine?
On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors
after autorecon2, and they have exclusively been segmentation faults. I¹m
running sta
Hi,
actually in the newer FS versions (don't know when it started), the
cortribbon is part of autorecon3. In those cases all that is necessary
is to rerun the final steps:
-cortribbon
-aparc2aseg
-wmparc
Martin
On Mon, 2009-08-03 at 14:18 -0400, Nathan Dankner wrote:
> Hello all,
>
> I’ve recen
Nathan,
This is a known and long-standing problem with mris_volmask. The fault
occurs deep within a library, VTK, of which we make use (null pointer in
vtkDataArrayTemplate::GetTuple). We're trying to find a fix or
workaround to this really annoying problem.
The cheap workaround is to run the -
Hi Geoffrey,
if you can put the data somewhere we can get to it someone here will take
a look.
Bruce
On Wed, 28 Apr 2004, Geoffrey Aguirre wrote:
> Folks --
>
> I'm working with a dog brain. With the help of Denis Fize, I've
> "tricked" freesurfer into treating my 0.47 mm voxels as 1 m
Folks --
I'm working with a dog brain. With the help of Denis Fize, I've
"tricked" freesurfer into treating my 0.47 mm voxels as 1 mm voxels,
and I have manually stripped the skull. I used the automated routine to
segment white matter and then manually erased the brainstem and
cerebellum. Now,
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