RES: [Freesurfer] Cannot allocate memory / can't allocate region
Check ulimit -m That's the max mem per process. ulimit -m 0 Maybe will help. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Jürgen Hänggi Enviada: 01/07/2009 02:36:36 Para: Freesurfer Mailinglist Assunto: [Freesurfer] Cannot allocate memory / can't allocate region Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice 000: dt: 0., sse=4822516.5, rms=2.25 rms = 2.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=4898456.5, rms=1.89 rms = 1.86, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=5293477.5, rms=1.86 045: dt: 0.1250, sse=5277681.5, rms=1.76 046: dt: 0.1250, sse=5237215.5, rms=1.70 rms = 1.69, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5270459.0, rms=1.69 positioning took 16.1 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... Cannot allocate memory Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jul 1 04:20:34 CEST 2009 [juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri] I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors 8192 The process terminated before all RAM is active and no swap is used. Any idea? Thanks in advance Regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RES: Re: [Freesurfer] Where can I read the manual for old freesurfer version (some new information)
Zhang In the wiki page there's a feature to check the previous version of each page. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Bruce Fischl Enviada: 29/06/2009 17:30:10 Para: Zhang, Xiaochu (NIH/NIDA) [F] Cc: 'freesurfer@nmr.mgh.harvard.edu' Assunto: Re: [Freesurfer] Where can I read the manual for old freesurfer version (some new information) I'm not sure we have it so easily. Does anyone know? On Mon, 29 Jun 2009, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > The freesurfer I am using now is this version, > "freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.4". I knew there is much > improved in the current version.However, I have about 80 participants done in > this old version. I only want to add several new participants and do some > group anlaysis. Today I read the wiki and found a lot of things in > "GroupAnalysis" have been changed. I tried to follow the new workflows but I > found it is not suit to old verison. Who can do me a favor and give me the > manual for the old version? My advisor asked me for result just now. > Thank you so much! > > > > Xiaochu Zhang PhD > Visiting Research Fellow > Neuroimaging Research Branch > National Institute on Drug Abuse - IRP > Biomedical Research Center > 251 Bayview Blvd. > Suite 200 (NIDA) > Baltimore MD > 21224 > Tel: 443-740-2619 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RES: [Freesurfer] volume group analysis
To make analysis of volumetric data export volumetric data to csv and use your statistical package. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Anita di Iasio Enviada: 25/06/2009 06:04:38 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] volume group analysis Hi all, I have 2 groups of subjects and I want to do a volume group analysis to compare volumes of subcortical structures. I have to run my analysis with the command-line methods but I don't know the correct flags to use with the commands (mris_preproc and mri_glmfit). Can you help me? Can you give me some suggestion? thank you in adavanced, Anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RES: [Freesurfer] qdec start
Jose. 1) Yes. You should run -qcache 2) Yes. This file is used to describe your experiment. You can have more details in the FreeSurfer tutorial for group analysis. PPJ -- Pedro Paulo Jr E71 Nokia -Msg original- De: Jose Soares Enviada: 15/06/2009 06:38:02 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] qdec start Hi all, I am starting with qdec and i have a simple question. I have 30 recon-all subjects but I didn't do the -qcache option. 1- I want to know if I need to run this -qcache option even if I use the fsaverage target subject, or this is only necessary if se my own average subject? 2- Where do I make the connection between my subjetcs and qdec? It is only in qdec.table.dat? Thanks for the help, Miguel. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] GM
Aseg.stat Sent from my Nokia phone @E71 -Original Message- From: Gabriel Go.Es. Sent: 30/03/2009 07:14:32 Subject: [Freesurfer] GM hello I want to use GM volume stats, i don't know whether it is or not, where? I had understood that FS does not calculate the total GM volume, how can I make it? and can I calculate it for an individual ROI on a specific area? Regards Gabriel _ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: Res: [Freesurfer] Doubt about GM
Did you check aseg.stat Sent from my Nokia phone @E71 -Original Message- From: Kelly Silva Sent: 30/03/2009 05:46:36 To: Bruce Fischl Cc: freesurfer Subject: Res: [Freesurfer] Doubt about GM Hello, Thank you for your answer, Bruce. I am looking for the colheader that brings the total GM and the GM for each hemisphere, but I did not find. Can you tell me how its the file and how is the name of the variable? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] merging rh and lh surfaces
I think Bruce or Douglas can explain better. However, the reason for both hemispheres being separated is that you need to mantain an S2 topological space. Sent from my Nokia phone @E71 -Original Message- From: s...@nmr.mgh.harvard.edu Sent: 19/03/2009 19:07:48 Subject: [Freesurfer] merging rh and lh surfaces Hi, I would like to have a single surf file that composed of both right and left pial surf. Is there a way to do it in freesurfer? Best. seok -- Seok Lew, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail s...@nmr.mgh.harvard.edu FAX 617 726 7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] brazil course
We still have four places. Sent from my Nokia phone -Original Message- From: Nick Schmansky Sent: 17/02/2009 18:36:08 To: Sam Torrisi Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] brazil course Sam, Pedro Paulo de M. Oliveira's email is: ppj at netfilter.com.br The original post is here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009- February/009688.html with details here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/BrazilCourseSchedule A course is being offered in Boston in April, but its already full. You can register for it anyway to be put on the waiting list for that course or future courses. That course description and link to the registration page is here: http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription There will likely be a one-day Freesurfer component to an FSL course that might be offered in San Francisco just before HBM in June, but you'll have to monitor the FSL site to check on the status of that (and noting that the Freesurfer component is not separate from the main FSL course). Nick On Tue, 2009-02-17 at 13:11 -0800, Sam Torrisi wrote: > hello there, > > i have questions for Pedro Paulo de M. Oliveira regarding the upcoming > Brazilian FS course but cannot find his email address anywhere in the > archives or his announcement. also, do you know if there is another > upcoming course in the states, preferably on the west coast? thank you > > -Sam Torrisi > > Neuroscience IDP PhD student > University of California Los Angeles > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cluster on Demand
Hi, That's good. Quotes from the site below. Maybe creating a VO for FreeSurfer users is an idea. Best Regards, PPJ ""I want to use OSG resources." OSG does not currently support individual researchers. Rather, users of the OSG are required to band together into Virtual Organizations (VOs). The VO-based security infrastructure of OSG is probably the most important reason for this policy, although by no means the only. OSG operates much as a "wholesaler" network, and VOs are expected to provide the "retailer" functions to their users, e.g., user support, application debugging, and so on. Therefore, to access OSG resources you must join a VO. OSG offers three options: If you are an individual or small group wanting to use the OSG for your independent research, you may join OSG’s general-purpose VO named, confusingly(!), OSG. Send email to Goc at opensciencegrid dot org requesting admission to the “OSG” VO. Join an existing member VO (See the list of current OSG VOs ) whose scope includes the applications you want to run (e.g., OSGEDU – the education VO for students and teachers). To join an existing VO you need to contact its Support Center. Check the List of Support Centers and problem reporting addresses to find your Support Center. If you have questions, ask Goc at opensciencegrid dot org. Form a new VO for your research community and register it with OSG. This process is described below. Once you're in a VO, you'll need to run your application. Some VOs provide an interface for you (you'll need to check with your VO support center and your application administrator in that case). For information on running jobs, navigate from the Technical documentation hub. " On Wed, 26 Mar 2008 17:22:56 -0500, "U. Hasson" <[EMAIL PROTECTED]> wrote: > Pedro, > > That's right. I should have realized that from the name / email address. > > However, the good news is that the open science grid (OSG) doesn't > have this limitation. http://www.opensciencegrid.org/. > They do have foreign users. The principle there is that they expect > users to share their own resources or otherwise contribute to the > enterprise if sharing local resources is not an option. > > Uri > > On Wed, Mar 26, 2008 at 11:25 AM, Pedro Paulo Oliveira Jr > <[EMAIL PROTECTED]> wrote: >> Hi, >> >> I entered Teragrid web and I saw this info: >> >> " To qualify for an award, the principal investigator (PI) must be a >> researcher or educator at a U.S. academic or non-profit research >> institution. A qualified advisor may apply for an allocation for his or > her >> class, but a high school, undergraduate or graduate student may not be > a PI. >> A postdoctoral researcher can also be a PI. (After receiving an award, > PIs >> can request that students be granted accounts to use the PI's > allocation.) >> >> In general, TeraGrids follow the guidelines outlined in the current NSF >> Grant Proposal Guide. However, investigators with support from any > funding >> source, not just NSF, are encouraged to apply. If your institution is > not a >> university or a 2- or 4-year college, special rules may apply. Contact >> [EMAIL PROTECTED] for details." >> >> Since I'm outside US I believe I'm not elegible. Is that right? >> >> Tks >> >> PPJ >> >> >> -Original Message- >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of U. > Hasson >> Sent: quarta-feira, 26 de março de 2008 13:08 >> To: Pedro Paulo Oliveira Jr >> Cc: Freesurfer Mailing List >> Subject: Re: [Freesurfer] Cluster on Demand >> >> >> >> You might consider applying for a (free) Teragrid account with which >> you can relatively easily obtain 30 thousand CPU hours in a >> Development Allocation. We're using a few allocations for neuroimaging >> analysis workflows including FreeSurfer. Just to understand, would >> they have charged you 33*100*0.75 ($2475) dollars for this? >> >> See: >> http://www.teragrid.org/userinfo/getting_started.php >> >> >> On Wed, Mar 26, 2008 at 10:33 AM, Pedro Paulo Oliveira Jr >> <[EMAIL PROTECTED]> wrote: >> > >> > >> > >> > >> > Dear Freesurfers >> > >> > >> > >> > I was testing a Cluster-on demand, pay-per-hour-used service US based > and >> it >> > seems pretty good. I ran 100 recon-all in 33 hours!!! >> > >> > >> >
[Freesurfer] Regarding QDEC Figure
In the attached figure: The numbers (-28.25, -12.73, -0.57) refer to fsaverage. How can I export the Thickness values of the subjects for this cordinates? The numbers (-28.25, -12.73, -0.57) are in Talairach space? Thanks, PPJ<>___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Two questions regarding Matlab
1) Two procedures:
a) set the variables: FREESURFER_HOME and FSFAST_HOME
b) Paste these lines in Octave:
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
path(path,fsmatlab);
clear fshome fsmatlab;
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
path(path,fsfasttoolbox);
clear fsfasthome fsfasttoolbox;
On Wed, 19 Dec 2007 19:49:35 -0200, "Pedro Paulo Oliveira Jr"
<[EMAIL PROTECTED]> wrote:
> Sorry for the stupid questions, I promise to put it on the FAQ after the
> answers:
>
>
>
> 1) Is it possible to use Octave instead Matlab for curv files?
>
> 2) Given a Talairach coordinate how can I get the thickness value in
> Matlab?
>
> Thanks in advance
>
>
>
> Pedro Paulo Jr
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Re: [Freesurfer] OpenGL, GLX, X11, VNC with FreeSurfer
Hi, FreeSurfer rendering under VNC is very slow and sometimes not possible. You may try UltraVNC (freeware - worked with me once) that has a better OpenGL support. I strongly recommend that you install a local copy of FreeSurfer and use it to visualize the data. Best Regards, Pedro Paulo Oliveira Jr On Fri, 14 Sep 2007 16:16:54 -0600, Troy Mcan <[EMAIL PROTECTED]> wrote: > Hi All, > > I'm trying to connect to a computer remotely to use freesurfer. However, > when I log in and try to load up a surface in freesurfer, I get the > following message: > > -No glx extension! > -Surfer: failed, trying double buffered window > -Xlib: extension "GLX" missing on display "computer name" > -Window type not found! > -Surfer: failed, no suitable display found > > I am using a VNC viewer (from www.realvnc.com) to log into the computer. > Are there any software rendering solutions for freesurfer so the VNC > doesn't run into the openGL problems? Or, on the other hand, are there any > VNC clients that are known to work with freesurfer? > > Thank you very much! > > > > _ > Gear up for Halo® 3 with free downloads and an exclusive offer. It’s > our way of saying thanks for using Windows Live™. > http://gethalo3gear.com?ocid=SeptemberWLHalo3_WLHMTxt_2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] running time v4
Hi, I would like to ask if there's already a benchmark performance of V4 compared to V3. In my environment V3 run a full recon-all in 21 hours full brain. How long I should expect the running time of V4 if I install it? Thanks, Pedro Paulo Oliveira Jr. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] read_surf error under Matlab R14 Linux
Hi,
I was using Matlab R14 in Linux to read a surface and compute a thickness
histogram.
I noticed that the read_surf function fails in every lh.thickness or
rh.thickness file. Even in bert dataset.
Here the error:
[vertex,f] = read_surf
('/usr/local/freesurfer/subjects/p111/surf/lh.thickness');
??? Subscripted assignment dimension mismatch.
Error in ==> read_surf at 41
faces(i,n) = fread3(fid) ;
I'm using Freesurfer 3.0.5
Thanks,
Pedro Paulo Oliveira Jr.
P.S. - I know that this issue has been previously discussed here but I have
patients with a cortex thickness larger than 5mm and the truncation makes
the statistical calculation fault in some aspects of my work. It would be
possible to have a "raw thickness" calculation?
Tks again
PPJ
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