Re: [Freesurfer] Memory problem

ard.edu] > Sent: Wednesday, January 23, 2013 1:45 PM > To: Douglas N Greve > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Memory problem > > Mia, > > also i noticed this at the top of the log: > > total used free > Mem: 3701

Re: [Freesurfer] Memory problem

Mia, also i noticed this at the top of the log: total used free Mem: 37010736 19490372 17520364 -/+ buffers/cache: 10784236 26226500 Swap: 8393952 1505288243424 it shows that just 1.7GB is available for the recon to run, which is belo

Re: [Freesurfer] Memory problem

Hi Mia, try looking at the lh.orig.nofix surface. There may be a huge defect (like the entire cerebellum is attached). You can run tkmedit MG58_SurferOutput_postop orig.mgz lh.orig.nofix Note that you will get a few error messages when loading the orig.nofix surface. These can be ignored doug

Re: [Freesurfer] Memory problem with mri_glmfit

It has to be float because that's what it uses internally. Can you break the volume up into slices? If so, then you can analyze each separately then combine the results back together (can't do correction for multiple comparisons though). doug On 5/11/11 10:19 AM, Bruce Fischl wrote: > no easy

Re: [Freesurfer] Memory problem with mri_glmfit

no easy one that springs to mind, sorry. Doug: any ideas? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: > OK, so there's no workaround from your side? > > There are many empty voxels in the volumes, > so as a workaround I'm going to crop the volumes > and hope that they will fit in the 2GB.

Re: [Freesurfer] Memory problem with mri_glmfit

OK, so there's no workaround from your side? There are many empty voxels in the volumes, so as a workaround I'm going to crop the volumes and hope that they will fit in the 2GB. On 11 May 2011, at 15:51, Bruce Fischl wrote: > oh, yes, that's definitely not enough: > > 4*256*256*256*72/(1024*10

Re: [Freesurfer] Memory problem with mri_glmfit

oh, yes, that's definitely not enough: 4*256*256*256*72/(1024*1024) ans = 4608 >> On Wed, 11 May 2011, Ed Gronenschild wrote: > I did. > However, without any other concurrent process > running I get exactly the same problem. I guess > that this is due to the 2GB limit which can be >

Re: [Freesurfer] Memory problem with mri_glmfit

I did. However, without any other concurrent process running I get exactly the same problem. I guess that this is due to the 2GB limit which can be allocated on a 32 bits machine. On 11 May 2011, at 15:40, Bruce Fischl wrote: > do you have other stuff running? > > On Wed, 11 May 2011, Ed Gronensc

Re: [Freesurfer] Memory problem with mri_glmfit

do you have other stuff running? On Wed, 11 May 2011, Ed Gronenschild wrote: > 16 GB > > On 11 May 2011, at 15:24, Bruce Fischl wrote: > >> Hi Ed, >> >> how much RAM do you have in your machine? >> Bruce >> >> >> On Wed, 11 May 2011, Ed >> Gronenschild wrote: >> >>> Hi, >>> >>> We are on a I

Re: [Freesurfer] Memory problem with mri_glmfit

16 GB On 11 May 2011, at 15:24, Bruce Fischl wrote: > Hi Ed, > > how much RAM do you have in your machine? > Bruce > > > On Wed, 11 May 2011, Ed > Gronenschild wrote: > >> Hi, >> >> We are on a Intel Mac and are facing a memory problem with >> mri_glmfit. >> We want to apply it to a 4D volume c

Re: [Freesurfer] Memory problem with mri_glmfit

Hi Ed, how much RAM do you have in your machine? Bruce On Wed, 11 May 2011, Ed Gronenschild wrote: > Hi, > > We are on a Intel Mac and are facing a memory problem with mri_glmfit. > We want to apply it to a 4D volume consisting of 72 3D volumes > of 256 * 256 * 256 voxels each, with 1 byte pe

[Freesurfer] Memory problem with mri_glmfit

Hi, We are on a Intel Mac and are facing a memory problem with mri_glmfit. We want to apply it to a 4D volume consisting of 72 3D volumes of 256 * 256 * 256 voxels each, with 1 byte per voxel. During processing we get the error message that it could not allocate 262144 bytes for the 9313th slice.

Re: [Freesurfer] Memory Problem when running mris_volmask

Hi Nick, After a long morning of looking through everything that was running on the computer, I finally made it work after: (1) Stopping some of the processes that were taking more memory. (2) Cleaning some stuff on the / filesystem. In fact I think this second point might have been the big

Re: [Freesurfer] Memory Problem when running mris_volmask

Javier, Does mri_convert output .mgz files? What OS is being used? If mri_convert doesnt produce .mgz files, then I don't know what to suggest. Nick On Wed, 2008-03-05 at 12:22 -0500, [EMAIL PROTECTED] wrote: > The output of gzip --version is: > > gzip 1.3.12 > Copyright (C) 2007 Free Softwa

Re: [Freesurfer] Memory Problem when running mris_volmask

The output of gzip --version is: gzip 1.3.12 Copyright (C) 2007 Free Software Foundation, Inc. Copyright (C) 1993 Jean-loup Gailly. This is free software. You may redistribute copies of it under the terms of the GNU General Public License . There is NO WARRAN

Re: [Freesurfer] Memory Problem when running mris_volmask

Javier, Which gzip version is being used? (gzip --version) Nick On Wed, 2008-03-05 at 11:54 -0500, [EMAIL PROTECTED] wrote: > Hi Nick, > > I checked disk space and there are still 59G available, so that should not be > the problem. > > About RAM this system has 3GB. > > Any idea of what

Re: [Freesurfer] Memory Problem when running mris_volmask

Hi Nick, I checked disk space and there are still 59G available, so that should not be the problem. About RAM this system has 3GB. Any idea of what might be going on? Thanks a lot, Javier. Quoting Nick Schmansky <[EMAIL PROTECTED]>: > Javier, > > It should not be necessary to revert to

Re: [Freesurfer] Memory Problem when running mris_volmask

Javier, It should not be necessary to revert to using COR files. How much memory and disk space do you have? We recommend 2GB of ram (and make sure disk space is not empty...freesurfer can fill-up a disk quickly). Nick On Wed, 2008-03-05 at 10:28 -0500, [EMAIL PROTECTED] wrote: > Hello, > >

[Freesurfer] Memory Problem when running mris_volmask

Hello, When I run the command "mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance DK1" I get the following error: ERROR: opening pipe gzip -f -c > /home/hammer/a/gonzalj/MirrorNeurons//DK1/mri/lh.dpial.ribbon.mgz,