to clarify: we are pretty sure it will either fail or run slowly, or both :)

Bruce On Tue, 21 Sep 2010, Douglas N Greve wrote:

It should just run slowly

doug

O'Shea, Colin (NIH/NIMH) [V] wrote:

...

I realize that FreeSurfer requires at least 4 GB RAM, and I?m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)?

Thanks,

Colin

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I got the following error when running isxconcat-sess:

ERROR: cannot find /space/grouch/3/users/ext/fsaverage/mri.2mm/subcort.mask.mgz

I've never seen this before, but this is my first time using isxconcat in fsfast v. 5.

Anyone know how to fix it?

Hi Folks, As Nick suggested 4GB per subject is best.

Here is my recent experience when memory resources may be limited and 4gb per subject is not available. I ran FS v5.0 on a cluster on which I was assigned a node with 16 cores and 32gb .

At a time, I am charged for all 16 cores on the node, whether I use them all or not; so i am trying to maximize the number of jobs I can submit. I have the option of submitting 8,12,15 or 16 jobs (subjects) on the node (using the -pe flag in the sun grid engine)

Depending on the number of jobs the 32gb is divided equally among the jobs; thus, if I submit 16 jobs, each job is assigned 2gb; if I submit 8 jobs, each jobs is assigned 4gb.

I found that if I submit 16 or 15 jobs, about half of them fail for me; If I submit 12 jobs, 2.66gb (32/12) is assigned to each subject and in this case most of jobs complete successfully; Out of more than 500 subjects only 3-4 cases failed if I assigned 2.66gb per subject.

hope this helps... Mehul

On Tue, Sep 21, 2010 at 7:32 AM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:

the visualization tools will work with just 1GB (or less) ram. its the recon-all stream that consumes a lot of memory. 2GB might work on when processing some subjects, but 4GB is best. it will fail midway through the processing stream if there is not enough memory (during mri_ca_register).

n.

On Tue, 2010-09-21 at 09:29 -0400, O'Shea, Colin (NIH/NIMH) [V] wrote:

...

I realize that FreeSurfer requires at least 4 GB RAM, and I’m in the process of getting extra ram for my computer. If I install FreeSurfer now, will the program simply not work or just run slow (or something in between)?

Thanks,

Colin

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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