24 Jul
2013
24 Jul
'13
11:42 a.m.
Hello Amir,
According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are encountering a memory error? If so, why?
-Zeke
On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log
On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: Hi, The content is : freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>> wrote: Hello Amirhossein, Can you please provide me with the contents of build-stamp.txt in the /Applications/freesurfer directory? -Zeke On 07/22/2013 04:23 PM, amirhossein manzouri wrote: Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.____edu/pipermail//freesurfer/____2011-July/019392.html <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/019392.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html>> Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__>> wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.______edu/fswiki/FsTutorial/____Tracula <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula> <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula>>> Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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 <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri