I see. We usually have 2mm isotropic diffusion voxels and an order of magnitude fewer voxels in the mask. So the high memory requirement here has to do with the high resolution of your data. These bedpost output files that it's trying to read in have 50 frames each, so you have to multiply that with the number of mask voxels to get an idea of the memory requirement.
On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > Hi - The voxel dimensions are 1.0156 x 1.0156 x 2.6 mm in the merged_f1 > bedpost output and the total number of voxels in the nodif_brain_mask is > 3,276,800. > > Ammar > ________________________________________ > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Friday, September 23, 2011 11:41 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Tracula Memory Requirements > > Hi Ammar - Can you check the voxel dimensions of one of the merged_* files > in the bedpost directory, and also how many voxels are included in the > mask that was used for bedpost? It seems to be failing when loading the > bedpost outputs, which is before it reads any tracula-specific inputs. > > a.y > > On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: > >> Hi Anastasia, >> >> These are both linux ubuntu 10.04 lts machines. The DICOM images are 1300 >> slices each 140 KB. >> >> Thanks, >> >> Ammar >> ________________________________________ >> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] >> Sent: Friday, September 23, 2011 10:30 AM >> To: Moiyadi, Ammar >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Tracula Memory Requirements >> >> Hi Ammar - Are these macos or linux machines and what is the size of your >> diffusion images? >> >> a.y >> >> On Fri, 23 Sep 2011, Moiyadi, Ammar wrote: >> >>> Hi Freesurfers, >>> >>> I've been getting a memory allocation error (below) when running trac >>> prep and trac paths on my computer with 6 gb ram. Since I was able to >>> run these steps on a computer with 16 gb, I want to know, what is the >>> minimum memory requirement for running tracula? Is the memory >>> allocation error resulting from a lack of memory or is there something >>> else going on that I am not aware of? >>> >>> Error: >>> >>> Loading BEDPOST parameter samples from >>> /usr/local/freesurfer5.1/subjects/1052/dmri.bedpostX MRIalloc(256, 256, >>> 50): could not allocate 262144 bytes for 431th slice >>> >>> Thanks always, >>> >>> Ammar Moiyadi, BS >>> Professional Research Assistant >>> Department of Psychiatry >>> University of Colorado Anschutz Medical Campus >>> 303-724-5490 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
