Thanks. I just added it into our code, so new versions will not have this problem. doug

Maryam Vaziri Pashkam wrote:

Hi,

Following up on the preprocessing error:

...

Can't connect? tcp_connect[connect]: Connection timed out

We figured where the problem is. This error came out when freesurfer calls an afni function. Apparently it tries to check which version of afni it is using against the internet to find out the most recent version. Suppressing the afni version check solved the problem. I just added this line to my .bashrc file: export AFNI_VERSION_CHECK=NO

Maryam

On Mon, Dec 12, 2011 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

  1. preprocessing error (Maryam Vaziri Pashkam)
  2. Re: preprocessing error (Douglas Greve)
  3. convert surface label on to functional image (Zhangyuanchao)
  4. References/materials for interaction analysis in  freesurfer
     (Bhavani Shankara Bagepally)
  5. Re: dt_recon error (Yuko Yotsumoto)
  6. Re: dt_recon error (Yuko Yotsumoto)
  7. Re: run preproc-sess with -nomc (Thunell Evelina)
  8. Re: mri_ca_register from virtual box (Lorenzo Busti)
  9. Re: mri_ca_register from virtual box (Lorenzo Busti)
 10. Converting thickness maps to vtk (Navid Shiee)
 11. Re: tracula and snow leopard: can't allocate region /     memory
     error (Anastasia Yendiki)
 12. tracula failed to find header file for -t (Scott Hayes)


----------------------------------------------------------------------

Message: 1
Date: Sun, 11 Dec 2011 14:34:05 -0500
From: Maryam Vaziri Pashkam <mvaziri.p@gmail.com
<mailto:mvaziri.p@gmail.com>>
Subject: [Freesurfer] preprocessing error
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:

 <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw@mail.gmail.com
<mailto:CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz%2B7sVrVBTjw@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

I am running preprocessing on my data using freesurfer 5.1, fsl
4.1.7, and
matlab R2009a (I also tried it with matlab 2007a) on Harvard
cluster and I
am receiving an error. I connect to the cluster using terminal and SSH
connection in mac.

the preprocessing is stalled in the middle with this error:

++ Max displacement in automask = 0.79 (mm) at sub-brick 3
Can't connect? tcp_connect[connect]: Connection timed out
++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz
** Warning: overwriting file 004/fmcpr.mcdat
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out


It does not stop running and output an error. But rather keeps
printing the
last line and does not move forward. Any idea where the problem
might be?


Thanks,
Maryam