Hi all,
After running a surface through autorecon2 and checking it I noticed that it
is tilted up at approximately a 45 degree angle. Is this a problem? If so,
how should I go about fixing it?
Nathan
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rom the
> machine running recon-all.
>
> From: Scott Burns [sbu...@nmr.mgh.harvard.edu]
> Sent: Tuesday, December 14, 2010 9:54 PM
> To: Watson, Christopher
> Cc: Nathan Dankner; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] runni
Hi All,
I'm running freesurfer on a public station, so I need to sign out when I'm
finished with sessions. Has anyone found a suitable way to run freesurfer
in the background? I know that I can run matlab in the background here, so
if there is a way to run the pipeline through matlab that may wo
> Can you send the result of
> cat $FREESURFER_HOME/build-stamp.txt
>
>
> Nathan Dankner wrote:
>
>> Oh sorry. I downloaded the CentOS 64-bit linux file, which should match
>> my platform...
>>
>> On Thu, Dec 2, 2010 at 5:06 PM, Dougl
es not
> match your platform then it will generate that error.
>
> doug
>
> Nathan Dankner wrote:
>
>> I downloaded version 5, and installed it into my home directory, as
>> opposed to user/local... I don't know if that's an issue or not
>>
>&g
I downloaded version 5, and installed it into my home directory, as opposed
to user/local... I don't know if that's an issue or not
On Thu, Dec 2, 2010 at 4:43 PM, Douglas N Greve
wrote:
> what version did you download?
>
> Nathan Dankner wrote:
>
>> Hi All,
>>
Hi All,
I've just installed freesurfer onto a linux node, and immediately
encountered a problem when trying to run my first scan. After executing the
recon-all command, the terminal spits out a string of errors saying:
[freesurfer home path]/mri_convert: Exec format error. Binary file not
execu
Hi all,
I've run into a recurring error with some scans that I am running. It is
duplicated below:
ncopen: filename "./tmp.mri_nu_correct.mni.8091/0/nu1_residue.mnc": Not
a netCD$
miopen: MINC package entry point
nu_estimate_np_and_em: crashed while running mincmath (termination
status=768)
nu_c
Hi all,
I was curious as to approximately how much memory is required to run a
surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them
on a new server where I have to request resources, so a ballpark figure is
really all I need. Thanks!
Nathan
ought 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
hine?
> 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 stable version 4.2 on a machi
Hello all. I am considering using peak activation voxels (with coordinates
either in talairach or MNI space) gleaned from fmri studies in our lab to
determine a priori areas of interest for examining group differences in
cortical thickness. Is this something that is possible in freesurfer? In
pa
Doug,
The Linux distribution I am using is equivalent to Redhat 5, and I am
running this on freesurfer version 4.2.0. The script I ran was
mri_glmfit-sim-mc-z.abs.2, which the qdec gui output for me. I believe I
attempted it with 6000 iterations. Do you need any more info? It seems the
other t
I have a couple of questions regarding the stats files. First, at the
beginning of the aparc.stats tables, there is a measure that is labeled
³unknown.² Is this total average thickness throughout the cortex, or just
some throw-away measure?
Secondly, I have heard that there are command line flag
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