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.eduwrote:
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Today's Topics:
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Message: 1 Date: Sun, 11 Dec 2011 14:34:05 -0500 From: Maryam Vaziri Pashkam mvaziri.p@gmail.com Subject: [Freesurfer] preprocessing error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAEEXA4cePaYDO8EPMpma7ThADfnd1qcYfg2HnnHz+7sVrVBTjw@mail.gmail.com
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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