External Email - Use Caution
Hi there,
yes, I can open an MRI volume just fine, using the code
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
But when it comes to surface files, it opens some of the surface files
while crashing with other ones.
Do you happen to know anything about
Can you load a MRI volume? From the crash report, it seems to be a system
related issue that triggered the crash.
Ruopeng
On Oct 26, 2023, at 8:42 PM, Mirsol Choi
mailto:mir...@ualberta.ca>> wrote:
External Email - Use Caution
Hi there,
I have processed a t1 image using recon-all fu
External Email - Use Caution
If you have been launching Freeview using the Finder by double clicking on the
icon, then try running it from the command line in a terminal to open a file,
e.g. in bash or zsh ...
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ source
$FREE
External Email - Use Caution
Are you using a second monitor, i.e., additional monitor besides the primary
one? There have been issues with images being displayed properly when
using multiple monitors with MacOS. I would first try everything on the
primary monitor (disconnect
] infant freesurfer crash
External Email - Use Caution
I am able to run infant freesurfer on my local pc but when I run on a cluster I
get segmentation error when running sscn_skullstrip.
Segment error in
$ sscnn_skullstrip -i
/cluster/projects/nn9208k/007_fs/work
External Email - Use Caution
I am able to run infant freesurfer on my local pc but when I run on a cluster I
get segmentation error when running sscn_skullstrip.
Segment error in
$ sscnn_skullstrip -i
/cluster/projects/nn9208k/007_fs/work/mprage.nu.conf.nii.gz -o
/cluster/proj
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Hello,
Thanks a lot! When I do things like this, I am able to run freeview from
the terminal and the nii file loads without any issue!
When I run Freeview.app, by clicking on it in the mac os GUI, it crashes
when I try to load the nii file.
So that it
External Email - Use Caution
Hello Nikolai,
You could let us know what version of MacOS you are running, e.g.,
$ sw_versProductName: Mac OS X
ProductVersion: 10.15.7
BuildVersion: 19H1419
I would try setting the environment variable FS_LICENSE to the absolute path of
your lic
External Email - Use Caution
Hello,
Thank you for your help!
I have an old intel mac (not M1). I allowed Freeview to access all my disk.
I also put the license file and run the export commands (but not sure if it
useful to run freeview.app?). But still it crashes when I try to op
External Email - Use Caution
Hello Nikolai,
A posting from September lists some things you can try,
https://secure-web.cisco.com/1PKZyepuYOeN_yDWbDmVHAh4TMYVweK8V3VAatHz0Mcg8MjRJ78VA5EmH-d2PZcu3jDaAtyAeC5_mmtWLperJeNw9XLDG1Dq4JHssVgS6mJEQ7lpsM_7C2Mdl0RpAWLjSF17e2-e4lwfNNaBhZ8SGLAVk
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Hello,
I just installed freesurfer 7.2.0 on mac os 11.6 using the pkg. Freeview
opens, but as soon as I select a nii file to load, it crashes.
Here is the report I get:
https://secure-web.cisco.com/1S_Xfvu-lNCy7GOzAyxCVPdF0cy5djt33DYm0S7sznuCGb1FT-JzZk
r support list"
Gesendet: Mittwoch, 4. November 2015 08:07:44
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
With the FS 6 beta version the problem doesn't occur.
Cheers, Clara
- Ursprüngliche Mail -
Von: "Ruopeng Wang"
An: "Freesurfer support list&
With the FS 6 beta version the problem doesn't occur.
Cheers, Clara
- Ursprüngliche Mail -
Von: "Ruopeng Wang"
An: "Freesurfer support list"
Gesendet: Dienstag, 3. November 2015 18:03:52
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Try 6.0.0b
.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang"
> An: "Freesurfer support list"
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [F
heers, Clara
- Ursprüngliche Mail -
Von: "Ruopeng Wang"
An: "Freesurfer support list"
Gesendet: Dienstag, 3. November 2015 17:57:50
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
There was a bug in freeview in FS 5.3.0 that may have caused the crash. Cl
oned error message.
Cheers, Clara
- Ursprüngliche Mail -
Von: "Bruce Fischl"
An: "Freesurfer support list"
Gesendet: Dienstag, 3. November 2015 14:42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us e
42:25
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it
crash?
thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when
Hi Clara
can you send us the wm.mgz and tell us exactly what you did to make it
crash?
thahks
Bruce
On Tue, 3 Nov 2015, Clara Kühn wrote:
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save
changes to the wm.mgz. It closes immediately and
Dear FreeSurfer experts,
since last week I have the problem that FS (5.3.0) crashes when I try to save
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can
always restore it by renaming the temporary file (wm.mgz~) but it obviously
doen't save any changes.
I've tried d
*To:*
freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Crash on recon-all on
Macbook Pro (Mavericks
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>
harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Matthew Riddle
mailto:mrid...@nyspi.columbia.edu>>
*Sent:* Thursday, October 23, 2014 7:48 AM
*To:* freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Crash o
t;>>>>
>>>>> I am encountering the exact same problem on Yosemite (10.10). The log
>>>>> file is attached. Any ideas? I am pretty stumped.
>>>>>
>>>>>
>>>>> Anthony
>>>>>
>>>>>
>>>
etty stumped.
>>>>
>>>>
>>>> Anthony
>>>>
>>>>
>>>>
>>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>> on behalf of Matthew Ri
--------
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>>> on behalf of Matthew Riddle
>>>
>>> *Sent:* Thursday, October 23, 2014 7:48 AM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>&g
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Matthew Riddle
*Sent:* Thursday, October 23, 2014 7:48 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks
and Yosemite)
Dear Freesurfer Team,
I
ideas? I am pretty stumped.
Anthony
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Matthew Riddle
*Sent:* Thursday, October 23, 2014 7:48 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer
: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to
Yosemite, and I re-installed X11 after the upgrade, but I'm still experiencin
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 23, 2014 12:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and
Yosemite)
Interesting. Ive never encountered that issue before but Ive also never
conducted an ins
Interesting. Ive never encountered that issue before but Ive also never
conducted an install test on subject bert on Mavericks or Yosemite. Ill
take a look. Thanks for the update.
-Zeke
On 10/23/2014 12:03 PM, Matthew Riddle wrote:
> Hi Zeke,
>
> So I may have solved the issue. Since /applicati
Hi Zeke,
So I may have solved the issue. Since /applications is write protected by
default, I had to run the recon-all with sudo. But it seems like the
subroutines of recon-all don't inherit the permissions, so I moved my Subjects
directory to Documents, and then I can run recon-all without the
Matt,
Can you send me the actual recon-all.log file? It might be helpful for
me to diagnose the issue. Thanks.
-Zeke
On 10/23/2014 07:48 AM, Matthew Riddle wrote:
> Dear Freesurfer Team,
>
> I recently installed Freesurfer on a new Macbook pro, which was upgraded
> to Yosemite, and I re-install
Dear Freesurfer Team,
I recently installed Freesurfer on a new Macbook pro, which was upgraded to
Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing
an issue with freesurfer that I’m hoping you might have some idea about.
Just to test the install and see what my tota
Hi Lucio, you need to give us more information. Try looking at this web
site to find out what we need
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
On 8/25/14 7:03 AM, D'anna, Lucio wrote:
> Hi all,
>
> hope this email finds you well.
> I am a new user of this program. I tried to open
Hi all,
hope this email finds you well.
I am a new user of this program. I tried to open lh.thickness opening a load
surface but the program continues to crash.
Please can you help me?
Lucio
Lucio D'Anna
PhD Research Student
Forensic & Neurodevelopmental Science Department
Institute of Psychiat
When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all
-debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can send
the rest of the log.
Knut J
#--
#@# CA Reg Thu Sep 12 19:59:01 CEST 2013
/cluster/home/kjbjuland/freesurfer/long/NTN
Hi,
I have run recon-al longitudinal process on abel cluster with this command
recon-all -base @filename@_template -tp @filename@ -tp @filename@v2 -all
-debug. However, it crashed or is killed when it ran mri_ca_register.
I have looked through the log, and I have not found a reason for it being
Hi,
I have some trouble running recon-all longitudinal pipelines. When
recon-all comes to mri_register_ca it crashes without giving a message,
even tough 8g ram was available. I have run the program with -debug. Is
there any other option I may use? The system is running Rocks 6.0
(Mamba), and i
Hi Nate
how much RAM is there, not disk space.
cheers
Bruce
On Wed, 17 Apr 2013, Nate Lee wrote:
Hello Bruce,
The iMac has 500GB capacity, and 425GB is not in use.
Best regards,
Nate
On Wed, Apr 17, 2013 at 12:06 PM, Bruce Fischl
wrote:
Hi Nate
how much memory do you have
Hello Bruce,
The iMac has 500GB capacity, and 425GB is not in use.
Best regards,
Nate
On Wed, Apr 17, 2013 at 12:06 PM, Bruce Fischl
wrote:
> Hi Nate
>
> how much memory do you have in the machine?
> Bruce
>
> On Wed, 17 Apr 2013, Nate Lee wrote:
>
> Hello everyone,
>> I'm using Freesurfer
Hi Nate
how much memory do you have in the machine?
Bruce
On Wed, 17 Apr 2013, Nate Lee
wrote:
Hello everyone,
I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am
experiencing regular
crashes during these several occasions:
1. Opening more than two volumes at once
2. W
Hello everyone,
I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am
experiencing regular crashes during these several occasions:
1. Opening more than two volumes at once
2. When one volume and one surface is open and:
a. switching back and forth between different exposé d
Carl,
I see that is one of our Mac OS X builds (the toughest to get working),
we'll try to replicate. Thanks for passing along the info.
Nick
On Mon, 2013-01-07 at 15:50 -0500, Carl Anderson wrote:
> Hi Everyone,
> I did the full install for 5.2 but got the following crash during
> Talairach:
When I run subfield segmentation for some of the subject, I get segmentation
error. Is there any known workaround these problems as recon-all is ran on a
cluster? I usually get this error Rasterizing
Levenberg-Marquardt.../global/apps/freesurfer/5.1.0/bin/kvlSegmentHippocampalSubfields.sh:
line
Title: Freesurfer crash
Hi Ingo,
Sometimes when you click to open the file
menu you can actually click really quickly on quit, which can open up right under
your mouse depending on where all the windows are on the screen. Try
clicking and holding your mouse button down while the mean
Ingo,
Its likely not a hardware problem. tkmedit creates a file called
.xdebug_tkmedit. Can you send me that file? It contains debug
information.
Also, there is a sample subject, called 'bert', included with the
installation. Does it open that subject correctly?
Lastly, check the directory c
Title: Freesurfer crash
Hi everyone. I habe a rather obscure problem. After loading a volume with tkmedit, I tried to open the file menu via the file button in the menu bar and instanly freesurfer crashes. The software is installed on a Apple PowerMac OSX 10.4.6, Dual G5 2.5 GHz, Memory 2.5
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