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 [ayendiki@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.

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 [ayendiki@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 [ayendiki@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.

Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run into memory allocation problems running tracula preproc and paths with the error messages as follows:

************ 1. preproc error

Loading cortex mask from /usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz MRIalloc(218, 182, 182): could not allocate 872 bytes for 112th slice

Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux

trac-preproc exited with ERRORS at Fri Oct 7 12:33:56 MDT 2011

2. paths 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

Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux

trac-paths exited with ERRORS at Tue Oct 11 12:54:59 MDT 2011

***********

Has anyone else had these memory errors with their machines? I am running on a linux box ubuntu 10.04. When the code exits, the script is only utilizing about 20 percent of the memory so I am certain that the problem lies within my machine reading the code or within the code itself. Thank you in advance for any suggestions in solving this problem.

Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Moiyadi, Ammar Sent: Friday, September 23, 2011 12:31 PM To: Anastasia Yendiki Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements

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 [ayendiki@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 [ayendiki@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.

Hi - dmripaths used about 30 percent of the 16gb at max and than lowered to 6 percent. Dmri train uses about 25 percent of the 16gb throughout its process.

Would running the 32bit version of freesurfer have something to do with the problem? I have a PAE kernel installed to take advantage of the extra memory that the 32bit OS would otherwise not use. Is anyone else with a 32b linux box having memory errors?

Thanks,

Ammar ________________________________________ From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Tuesday, October 11, 2011 1:23 PM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements

Hi Ammar - You mentioned that you were able to run things fine on another computer with 16 Gb of RAM. How much memory was being utilized on that computer by these processes (dmri_train and dmri_paths)?

a.y

On Tue, 11 Oct 2011, Moiyadi, Ammar wrote:

Hi - After upgrading my total RAM to 12 gb (from 6) I am continuing to run into memory allocation problems running tracula preproc and paths with the error messages as follows:

---

1. preproc error

Loading cortex mask from /usr/local/freesurfer5.1/trctrain/trc010/dlabel/mni/cortex+2mm.nii.gz MRIalloc(218, 182, 182): could not allocate 872 bytes for 112th slice

Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux

trac-preproc exited with ERRORS at Fri Oct 7 12:33:56 MDT 2011

2. paths 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

Cannot allocate memory Linux coolguy 2.6.38-10-generic-pae #46~lucid1-Ubuntu SMP Wed Jul 6 20:34:59 UTC 2011 i686 GNU/Linux

trac-paths exited with ERRORS at Tue Oct 11 12:54:59 MDT 2011

---

Has anyone else had these memory errors with their machines? I am running on a linux box ubuntu 10.04. When the code exits, the script is only utilizing about 20 percent of the memory so I am certain that the problem lies within my machine reading the code or within the code itself. Thank you in advance for any suggestions in solving this problem.

Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Moiyadi, Ammar Sent: Friday, September 23, 2011 12:31 PM To: Anastasia Yendiki Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula Memory Requirements

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 [ayendiki@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 [ayendiki@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.