External Email - Use Caution
I looked through the thread and downloaded VirtualBox. Freesurfer 5.1
installation was working fine but mounting my drive and sharing folders
required so many libraries which are now defunct, it just wasn't worth it. I
wrangled with the machine for a while but it seems easier to just process
everything with freesurfer 7.4.
Thanks,
K
------- Original Message -------
On Monday, September 18th, 2023 at 8:02 AM, Huang, Yujing
<yhuan...@mgh.harvard.edu> wrote:
> External Email - Use Caution
>
> You are using Freesurfer 5.1
> (freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0). I’m wondering if it is
> software compatibility issue.
>
> There are suggestions on how to run Freesurfer 5.1 from container in this
> posting - [MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be
> https://secure-web.cisco.com/18JSemI8UZisRAbamkAD4iEpeHnPbUto45vp33zIyv6IxlxH6YY_ccXNVq1bmims4D73UhRQQc55skHaxr7mL7bmo19VXhughEQHs2oC_SgCBJM6Pspz18oq8ETY0yiZ1gy_iRlnnHVgzkRWKKBU7p8dUY_RNJ_fp0F9C4ruTUINzQs8aE-tbwUm-j7sbo67BsA1NUuAarLEtmv7TBc0UASWbPhDkfweJtDJ3L6B75NnbOyr3i0vR2CYwEgegY0UcJ8KS_XX7uqmR6GcFKyqky_Tz-Zpj_rxSLW8dM8V85Hz-FiK6aR0GUgu-JXHRsTQE/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html](https://secure-web.cisco.com/1zoee5Wuv_DvRaT0fpKqBwycBeglhqic772BD4C6VpO6izm3ko3HbKPFAhhiSvHUnH2VQsVbbE6SCsil2t_uZiXawtT72CtBfi8VIAFZuWUn25D4ubxeaap7woc9mG9Yy1Wu1Es0agG-DTknpF_Wehz_xUywjWQyLGqahiHTWbSDXkJDIkMD-VXedp_TMcIAgjTWyYdyMA1Vy2cRruqatwVaE03hCpnXnjrovVfhMKBXrWCBilDshe2qF6UT2gEt4/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74552.html)
>
> Hope this helps.
>
> Best,
>
> Yujing
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of KennethSPrice
> Sent: Sunday, September 17, 2023 11:35 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] mri_convert: Segmentation fault (core dumped)
> synthsr scan
>
> External Email - Use Caution
>
> I've set the coredumpsize to unlimited, and still get the same error. Could
> it be something with the installation?
>
> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> Linux DESKTOP-MRI 4.4.0-19041-Microsoft #3393-Microsoft Mon Aug 14 14:52:00
> PST 2023 x86_64 x86_64 x86_64 GNU/Linux
>
> cputime unlimited
>
> filesize unlimited
>
> datasize unlimited
>
> stacksize 8192 kbytes
>
> coredumpsize unlimited
>
> memoryuse unlimited
>
> vmemoryuse unlimited
>
> descriptors 1024
>
> memorylocked 64 kbytes
>
> maxproc 7823
>
> maxlocks unlimited
>
> maxsignal 7823
>
> maxmessage 819200
>
> maxnice 0
>
> maxrtprio 0
>
> maxrttime unlimited
>
> total used free shared buff/cache available
>
> Mem: 16643620 4264632 12149636 17720 229352 12245256
>
> Swap: 29192228 0 29192228
>
> ------- Original Message -------
> On Saturday, September 16th, 2023 at 9:49 PM, fsbuild <fsbu...@contbay.com>
> wrote:
>
>> External Email - Use Caution
>>
>> Hello Ken,
>>
>> The output from your linux shell limits in the log show the following,
>>
>> cputime unlimited
>>
>> filesize unlimited
>>
>> datasize unlimited
>>
>> stacksize 8192 kbytes
>>
>> coredumpsize 0 kbytes
>>
>> memoryuse unlimited
>>
>> vmemoryuse unlimited
>>
>> descriptors 1024
>>
>> memorylocked 64 kbytes
>>
>> maxproc 7823
>>
>> maxlocks unlimited
>>
>> maxsignal 7823
>>
>> maxmessage 819200
>>
>> maxnice 0
>>
>> maxrtprio 0
>>
>> maxrttime unlimited
>>
>> I would set at least coredumpsize to something non-zero so you can at least
>> get a core file saved that could be looked at. By default the limits on my
>> Ubuntu 22 system are:
>>
>> $ ulimit -a
>>
>> real-time non-blocking time(microseconds, -R) unlimited
>>
>> core file size(blocks, -c) unlimited
>>
>> data seg size (kbytes, -d) unlimited
>>
>> scheduling priority (-e) 0
>>
>> file size (blocks, -f) unlimited
>>
>> pending signals (-i) 378881
>>
>> max locked memory (kbytes, -l) 64
>>
>> max memory size (kbytes, -m) unlimited
>>
>> open files(-n) 1048576
>>
>> pipe size(512 bytes, -p) 8
>>
>> POSIX message queues (bytes, -q) 819200
>>
>> real-time priority(-r) 0
>>
>> stack size(kbytes, -s) 8192
>>
>> cpu time (seconds, -t) unlimited
>>
>> max user processes(-u) unlimited
>>
>> virtual memory(kbytes, -v) unlimited
>>
>> file locks(-x) unlimited
>>
>> You can try setting the core file size to unlimited with,
>>
>> $ ulimit -c unlimited
>>
>> ... then check the value was changed to something > 0 ...
>>
>> $ ulimit -a
>>
>> You could increase memory size (and as many shell limits as possible) to
>> unlimited to get the max size allowed by the system in the script you use to
>> run recon-all, and then try running recon-all again to see if you can
>> retrieve a core dump file.
>>
>> - R.
>>
>>> On Sep 16, 2023, at 09:55, KennethSPrice <kennethspr...@protonmail.com>
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> OK, I've attached the log file.
>>>
>>> ------- Original Message -------
>>> On Friday, September 15th, 2023 at 2:59 PM, fsbuild <fsbu...@contbay.com>
>>> wrote:
>>>
>>>> External Email - Use Caution
>>>>
>>>> It might help if you could send along the crash report as an attachment..
>>>>
>>>> -R.
>>>>
>>>>> On Sep 15, 2023, at 14:36, KennethSPrice <kennethspr...@protonmail.com>
>>>>> wrote:
>>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> Update: I tried running recon-all (5.1, ubuntu 18) on a sample MPRAGE
>>>>> scan and got the "mri_convert: segmentation fault (core dumped)" error
>>>>> again. Any clarity on this issue would be appreciated.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> K
>>>>>
>>>>> ------- Original Message -------
>>>>> On Thursday, September 14th, 2023 at 10:41 PM, KennethSPrice
>>>>> <kennethspr...@protonmail.com> wrote:
>>>>>
>>>>>> Howdy yall,
>>>>>>
>>>>>> I ran a subject through synthsr (freesurfer 7.4) and am trying to run
>>>>>> the output through the freesurfer 5.1 pipeline (the rest of my dataset
>>>>>> was processed with 5.1). I am getting the error "Segmentation fault
>>>>>> (core dumped)" during the mri_convert step. Any suggestions?
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Ken
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu
>>>>> [MailScanner has detected a possible fraud attempt from
>>>>> "secure-web.cisco.com" claiming to be
>>>>> https://secure-web.cisco.com/13BrdrDQK4pNPqanbnKRQ_ykyDtXv2umoChrgVicz4dKTIgzvXtb9dP7o7Jbf0KYowWdrX5Lgm7EpoOBOqam9u_FiQBqoGw6Jwo7YOnfDwZencuxBUvO4Jp8_yw6Lt7r99SEKTa5nourbgUQmvW_SeWOpM6XXxbXUx-KiVzg6GBSpHCnDyTj3P5cz5rMWj13-b0E2Feudrjdb0QD5dV85KjGv4yovMkOORRC8DPfSeMhXUogj8z42K7pSxIPw4mIyvEEOoExdFH5MEDmi96BqqPwHJQ3nFTPiLYJKmWQ0C2H_gsTpTj0nhTLiz25M15qn/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer](https://secure-web.cisco.com/1tAFJgrB-KsGn352qBMwxDWuyMY6TfPlYTyTSqAcvSZTIR2jrnGfKT3ICrDtrEkTauFnLddVh91GYTrHze6N4JzOcr0I70poRIjRTE7Rad8Dx_5hdBm2v0SSRknBx11ZhHTZ54I5RWrjnfZTAawmJ1tuFmHO6VgB-7SnR0HdmerhqdNN_tN9ouW812Q_9qwpMCwSYXWbGQNvDeAbeNRwyLujcY-q_0anFjR09MpMqqgYvqU4RaaqWGZBaG45wBV0m/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer)
>>>
>>> <recon-all.log>_______________________________________________
>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu
>>> [MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be
>>> https://secure-web.cisco.com/13BrdrDQK4pNPqanbnKRQ_ykyDtXv2umoChrgVicz4dKTIgzvXtb9dP7o7Jbf0KYowWdrX5Lgm7EpoOBOqam9u_FiQBqoGw6Jwo7YOnfDwZencuxBUvO4Jp8_yw6Lt7r99SEKTa5nourbgUQmvW_SeWOpM6XXxbXUx-KiVzg6GBSpHCnDyTj3P5cz5rMWj13-b0E2Feudrjdb0QD5dV85KjGv4yovMkOORRC8DPfSeMhXUogj8z42K7pSxIPw4mIyvEEOoExdFH5MEDmi96BqqPwHJQ3nFTPiLYJKmWQ0C2H_gsTpTj0nhTLiz25M15qn/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer](https://secure-web.cisco.com/1tAFJgrB-KsGn352qBMwxDWuyMY6TfPlYTyTSqAcvSZTIR2jrnGfKT3ICrDtrEkTauFnLddVh91GYTrHze6N4JzOcr0I70poRIjRTE7Rad8Dx_5hdBm2v0SSRknBx11ZhHTZ54I5RWrjnfZTAawmJ1tuFmHO6VgB-7SnR0HdmerhqdNN_tN9ouW812Q_9qwpMCwSYXWbGQNvDeAbeNRwyLujcY-q_0anFjR09MpMqqgYvqU4RaaqWGZBaG45wBV0m/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer)
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
