I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I actually think there is a problem of alignment  because the 3 T1s are quiet different from each other: they come from a patient affected by MS with a big lesion in the left frontal lobe. This lesion withdraws drastically in the last T1 as you can see from the two attachments. Moreover, I  got a problem in the recon-all, given that freesurfer was not able to reconstruct properly the pial and white surfaces (the gray matter is spared in the patient, however it is not included in the lh.pial surf). Do you think there is a way to edit the brainmask for such a big lesion? Would this solve the problems with the recon-all base?

Thank you!

----Messaggio originale----
Da: theniels@gmail.com
Data: 15-dic-2015 9.31
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] recon-all base error

Hi - how much memory do you have on your machine?

On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea.92@libero.it <salvatoreandrea.92@libero.it> wrote:

Hi Freesurfer experts!

I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error:

Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation
Cannot allocate memory
Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

I tried with a more powerful pc but I encountered the same problem.

Following further information:

SUBJECT template_base
DATE ven 11 dic 2015, 08.17.47, CET
USER salvatore
HOST salvatore-HP-630-Notebook-PC
PROCESSOR x86_64
OS Linux
Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
/home/salvatore/freesurfer/bin/recon-all
PWD /home/salvatore/freesurfer/subjects/template_base/scripts
CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh

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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
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