I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all? If it is not, do you know whether there is a way to split up the process?
----Messaggio originale----
Da: theniels@gmail.com
Data: 27-nov-2015 17.24
A: "salvatoreandrea.92@libero.it"salvatoreandrea.92@libero.it, "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] report a bug
Hi - sounds like it's running out of memory and getting killed. How much RAM do you have?
On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea.92@libero.it salvatoreandrea.92@libero.it wrote: Hi! - I am using Ubuntu 14.4 (trusty).
- This is my subject directory: /home/salvatore/freesurfer/subjects
- This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all
- The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all
Following the error that I got after 12 hours of processing:
sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64
setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET
Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you
Best,
Salvatore
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