Hi Mark,
Thank you so much for helping me resolve this problem.
Best Regards,
Dana
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Mark Jenkinson [[log in to unmask]]
Sent: Monday, February 15, 2010 12:03 PM
To: [log in to unmask]
Subject: Re: [FSL] FIRST Follow-Up Question
Dear Dana,
I see that in your log files you have:
dyld(4518) malloc: *** vm_allocate(size=8421376) failed (error
code=268435459)
dyld(4518) malloc: *** error: can't allocate region
dyld(4518) malloc: *** set a breakpoint in szone_error to debug
(standard_in) 2: parse error
in the file first.e313.10 (always check the log files with cat
313.logs/*.e* )
This seems to be the problem. Is the computer that you are using
short of memory or being used by many other users? It looks like
you've just run out of memory for this run, and that would explain why
you see this every now and again. Talk to the IT person at your end and
see if there is anything you can do to alleviate the memory issue. It
is
not something that we normally see, so is more likely to be fixed at
your
end.
All the best,
Mark
On 15 Feb 2010, at 00:05, Eldreth, Dana A. wrote:
> Hi Mark,
>
> Thanks again for your very helpful response.
>
> I tried to replicate this problem in several of the participants who
> generated it initially, but I haven't had any luck. My sample is
> about 115 subjects and I continue to run into this problem in other
> subjects. So far I've noticed it in about 20+ of our people. Do
> you think that I should be concerned about this, or do you think it
> may be due to something you've listed below? It sounds like I don't
> need to worry about it.
>
> Best Regards,
> Dana
>
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
> Of Mark Jenkinson [[log in to unmask]]
> Sent: Sunday, February 14, 2010 9:53 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FIRST Follow-Up Question
>
> Hi,
>
> I hadn't intended to look at this data as you said that the
> problem could not be replicated, and hence I assumed that
> this meant that it had gone away. Is this the case? Do you
> still see this problem? If you are not getting the problem
> anymore then it may have just been due to corrupt file
> writing, disk quotas, or other things which are not worth
> worrying about.
>
> All the best,
> Mark
>
>
> On 14 Feb 2010, at 14:48, Dana Eldreth wrote:
>
>> Hi Mark,
>>
>> Thanks for your response. If you wouldn't mind taking a look at the
>> data
>> that I put on your server that would be great. So you can see my
>> responses,
>> I've put them in CAPS.
>>
>> Your previous response: I haven't heard about that problem of one
>> run
>> failing but
>> a re-run working. If you have a dataset where you can replicate
>> this (by
>> taking a fresh copy of the original data and doing it all again)
>> then please
>> upload it for us to have
>> a look at.
>>
>> I COULDN'T REPLICATE THIS PROBLEM AS YOU HAVE SUGGESTED HERE WITH THE
>> ORIGINAL DATA, SO I UPLOADED A SUBJECT WHO INITIALLY DISPLAYED THIS
>> PROBLEM.
>> UPLOAD NUMBER: 701725. YOU WILL SEE THAT IN THE
>> 313_all_fast_firstseg file
>> THE RIGHT AMYDALA APPEARS APPROXIMATELY IN THE JAW AREA.
>>
>> Any help is greatly appreciated!
>>
>> Thanks again and have a good weekend!
>> Dana
>>
>>
>> All the best,
>> Mark
>>
>>
>> On 29 Jan 2010, at 14:23, Dana Eldreth wrote:
>>
>>> I was wondering if anyone else noticed this problem with FIRST on
>>> the newest
>>> release 4.1.5.
>>>
>>> First, I'd like to note that FSL 4.1.5 does an excellent job at
>>> boundary
>>> correction on our older brains. It's extremely impressive.
>>>
>>> 1. For some reason, this newest release occasionally does not
>>> accurately
>>> parcellate some structures correctly (e.g., hippocampus in the brain
>>> stem),
>>> but when I rerun it again it appears to fix the problem and the
>>> volumes are
>>> where they should be in the brain. The volume sizes are also
>>> relatively
>>> close to the volume sizes that I had in the earlier version of
>>> FIRST.
>>> Interestingly, the volumes that appear to be parcellated in the
>>> wrong area
>>> produce the same volume size as when FIRST produces the volumes in
>>> the
>>> correct location. Has anyone else noticed this, and should this be
>>> something that I should be concerned about?
>>>
>>> I also had another question associated with FIRST:
>>> 1. How can I tell how confident the program is that it has
>>> accurately
>>> identified a specific structure, or can I only tell via visual
>>> inspection
>>> using a neuroantaomical atlas?
>>>
>>> As always, thank you so much!
>>>
>>> Dana
>>>
>>
>
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