Hi,
I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space.
At the time I ran into trouble the free disk space was about 11 GByte. When I wanted to inspect the progress after a few hours I noticed that the disk has ran out of space. I couldn't do anything but restarting the MacPro. Then the disk space was again about 11 GByte. So I reran the subject with recon-all -autorecon2 -autorecon3 and it happened again. Inspecting the log files I noticed that both times the problem occurred at exactly the same stage in the pipeline: mris-topo-fixer.
Cheers, Ed
On 10 Mar 2016, at 10:41, <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc.
hth d
On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) <ed.gronenschild@maastrichtuniversity.nlmailto:ed.gronenschild@maastrichtuniversity.nl> wrote: Hi developers,
Could you please help me out on this problem. Should I upload the data?
Cheers, Ed
Begin forwarded message:
From: Ed Gronenschild <ed.gronenschild@maastrichtuniversity.nlmailto:ed.gronenschild@maastrichtuniversity.nl> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To: <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
Hi developers,
My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta
During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full.
Cheers, Ed