---------- Forwarded message ---------- From: Rui Lavrador ruilavrador@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask.
Rui
2012/7/12 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask?
a.y
On Thu, 12 Jul 2012, Rui Lavrador wrote:
Hi all,
I'm running tracula and when doing the step: trac-all -prior -c single_subject
After some time it gives this error:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice
Cannot allocate memory
I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions.
This happens many times? I need more memory?
Best regards,
-- Rui Lavrador
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/**compliancelinehttp://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 all,
I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files.
thanks
2012/7/16 Rui Lavrador ruilavrador@gmail.com
---------- Forwarded message ---------- From: Rui Lavrador ruilavrador@gmail.com Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask.
Rui
2012/7/12 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu
Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask?
a.y
On Thu, 12 Jul 2012, Rui Lavrador wrote:
Hi all,
I'm running tracula and when doing the step: trac-all -prior -c single_subject
After some time it gives this error:
MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice
Cannot allocate memory
I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions.
This happens many times? I need more memory?
Best regards,
-- Rui Lavrador
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/**compliancelinehttp://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.
-- Rui Lavrador
Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador@fmed.uc.pt e-mail2: ruilavrador@gmail.com
-- Rui Lavrador
Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador@fmed.uc.pt e-mail2: ruilavrador@gmail.com
Hi Rui - Just keep in mind that when you're removing lines from trainlist.txt, you're removing subjects from the atlas. So instead of using a tract atlas that's based on 33 subjects, you are now using a tract atlas based on as many subjects as the lines that remain in trainlist.txt.
a.y
On Tue, 17 Jul 2012, Rui Lavrador wrote:
Hi all,
I think I found the problem. I reduced the number of train files in the trainlist.txt file and it ran without errors. Maybe I will need more memory to run with all train files.
thanks
2012/7/16 Rui Lavrador ruilavrador@gmail.com
---------- Forwarded message ---------- From: Rui Lavrador <ruilavrador@gmail.com> Date: 2012/7/16 Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior To: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> Hi Anastasia, Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels inside of the brain mask. Rui 2012/7/12 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> Hi Rui - How many voxels are in your diffusion volume? How many of them are inside the mask? a.y On Thu, 12 Jul 2012, Rui Lavrador wrote: Hi all, I'm running tracula and when doing the step: trac-all -prior -c single_subject After some time it gives this error: MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice Cannot allocate memory I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is DTI with 64 directions. This happens many times? I need more memory? Best regards, -- Rui LavradorThe 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.
-- Rui Lavrador
Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador@fmed.uc.pt e-mail2: ruilavrador@gmail.com
-- Rui Lavrador
Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador@fmed.uc.pt e-mail2: ruilavrador@gmail.com
-- Rui Lavrador
Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-548 Coimbra, Portugal Phone: +351 964985485 e-mail: rui.lavrador@fmed.uc.pt e-mail2: ruilavrador@gmail.com
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Rui Lavrador