Dear Bruce and FS experts,I am running recon-all using the longitudinal stream. I have a question regarding the specific command line for recon-all using the -openmp flag and regarding the organizing directory of longitudinal data. I am using FS version 5.3 CentOS 6 and in a linux work station with two processors with 4 cores (8 cores total).As far as I understand I can use the openmp 8 flag. But I just wanted to confirm the exact command line would be [recon -all -s -openmp 8] ?Also, do I need to include this flag for importing the files: [e.g. recon-all -i ... -s -openmp 8 ...] One last query, is there any command lines for organizing the subjects in terms of time point 1 and time point 2 for each subject?Thank you,Pablo
Date: Tue, 26 Nov 2013 16:41:31 -0500 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
Hi Pablo
it also depends on how much ram it has. You should be able to run 1 significantly faster using the -openmp 8 flag to recon-all, or 8 (if you have enough ram, probably at least 32G)
cheers Bruce
On Tue, 26 Nov 2013, pablo najt wrote:
Dear Bruce,Last week I emailed with the question of how many recon -all separate subjects I could run in parallel with the FS version 5.3 for Cent
os
- You answered that this depends on how many cores my machine has.
I just found out that our workstation has two processors with 4 cores each (8 cores in total). Would you be able to tell me how many subjects could I run in parallel wit
h
our workstation? Thank you for your support, Pablo
Date: Thu, 21 Nov 2013 10:47:34 -0500 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
Hi Pablo
it depends on how many cores you have
Bruce On Thu, 21 Nov 2013, pablo najt wrote:
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I
a
m
wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a ti
me
and it took around 20 hours. Would I be able to run 6 subjects in parall
el
?
If so would this process still efficient or there is an optimum number? Thank you, Pablo
Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkaufman@nmr.mgh.harvard.edu To: garikoitz@gmail.com CC: pablonajt@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and
CentOS 6
I have to agree with Gari, I see no reason for you to not use the CentOS6 build.
-Zeke
On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote:
I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in a
ny
reason to not use this version in your CentOS 6, if you have some ot
he
r
requirements maybe Nick or Zeke could help you better, I am just an
us
er
:)
On Wed, Nov 20, 2013 at 6:47 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo
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From: garikoitz@gmail.com mailto:garikoitz@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablonajt@hotmail.com mailto:pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., & Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234).
for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari
On Wed, Nov 20, 2013 at 5:58 PM, pablo najt <pablonajt@hotmail.com mailto:pablonajt@hotmail.com> wrote:
Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo
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From: pablonajt@hotmail.com mailto:pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 +0000 Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6
Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel).
I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo
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